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6bn9

Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC

Method: X-RAY DIFFRACTION Dmax: 132.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA damage-binding protein 1,DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–395 Chain A； UniProt 706–1140 Not recorded Protein cereblon × 1 （Q96SW2） Bromodomain-containing protein 4 × 1 （O60885） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8) Resolution 4.38 Å R-free 0.301

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BN9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Chain F 1–1140（1140 aa）
Not recorded A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.316
3E0C Crystal Structure of DNA Damage-Binding protein 1(DDB1) Deposited 2008-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M Bis tris, pH 6.5,0.2 M Lithium sulfate, 25% PEG 3350, 1:6000 Protein:Chymotrypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.41 Å R-free 0.283
3EI1 Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14 % PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.278
3EI2 Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.268
3EI3 Structure of the hsDDB1-drDDB2 complex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.251
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3I7H Crystal Structure of DDB1 in Complex with the H-Box Motif of HBX Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.279
3I7K Crystal Structure of DDB1 in Complex with the H-Box Motif of WHX Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.271
3I7L Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2 Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.289
3I7N Crystal Structure of DDB1 in Complex with the H-Box Motif of WDTC1 Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.290
3I7O Crystal Structure of DDB1 in Complex with the H-Box Motif of IQWD1 Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.320
3I7P Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A Deposited 2009-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.301
3I89 Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR22 Deposited 2009-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.304
3I8C Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR21A Deposited 2009-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
3I8E Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A Deposited 2009-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.40 Å R-free 0.338
3I8E Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A Deposited 2009-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.40 Å R-free 0.338
4A08 Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1) Deposited 2011-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；100 MM MES, 25 MM NAOH, 18% PEG 350MME., pH 5.6
Resolution 3.00 Å R-free 0.294
4A09 Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2) Deposited 2011-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 21% PEG 200, pH 5.3
Resolution 3.10 Å R-free 0.308
4A0A Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.6 A resolution (CPD 3) Deposited 2011-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；100 MM MES, 28 MM NAOH, 16% PEG 350MME., pH 5.6
Resolution 3.60 Å R-free 0.347
4A0B Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4) Deposited 2011-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3
Resolution 3.80 Å R-free 0.319
4A0B Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4) Deposited 2011-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 1–1140（1140 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3
Resolution 3.80 Å R-free 0.319
4A0K STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX Deposited 2011-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.3；100MM TRIS-HCL PH 8.3, 33% PEG 200
Resolution 5.93 Å R-free 0.270
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A11 Structure of the hsDDB1-hsCSA complex Deposited 2011-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；1.4-1.58 M NAKPO4, 0.1 M NAMALONATE, 0-0.1 M LI2SO4, pH 8.0
Resolution 3.31 Å R-free 0.233
4CI1 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide Deposited 2013-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EF2 S-Thalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE; 80 MM NAH2PO4; 120 MM K2HPO4; 800 MM TRI-NA CITRATE., pH 6
Resolution 2.98 Å R-free 0.233
4CI2 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to lenalidomide Deposited 2013-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE PH 6.2, 80 MM NAH2PO4, 120 MM K2HPO4, 950 MM TRI-NA CITRATE.
Resolution 2.95 Å R-free 0.234
4CI3 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to Pomalidomide Deposited 2013-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACOCYLATE, 80 MM NAH2PO4, 120 MM K2HPO4, 700 MM TRI-NA CITRATE., pH 6.5
Resolution 3.50 Å R-free 0.235
4E54 Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 2–1140（1139 aa） Fragment：DNA DAMAGE-BINDING PROTEIN 1 (DDB1; p127)
Mutation：NT-His10-DDB1 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K
Resolution 2.85 Å R-free 0.281
4E5Z Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 2–1140（1139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K
Resolution 3.22 Å R-free 0.284
4TZ4 Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide Deposited 2014-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–1140（1139 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K
Resolution 3.01 Å R-free 0.271
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200mM NaCl, 20% PEG 3350
Resolution 3.20 Å R-free 0.267
6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.99 Å R-free 0.333
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
Resolution 6.34 Å R-free 0.381
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 3.33 Å R-free 0.234
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT
Resolution 3.09 Å R-free 0.307
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT
Resolution 3.09 Å R-free 0.307
6FCV Structure of the human DDB1-CSA complex Deposited 2017-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium citrate, 24% PEG 3350, 0.1 M bis-tris propane pH 8.0, 3% glycerol
Resolution 2.92 Å R-free 0.245
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6PAI Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820 Deposited 2019-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M sodium HEPES, pH 7.0, 15% w/v PEG4000
Resolution 2.90 Å R-free 0.252
6Q0R Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39 Deposited 2019-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded OXM OXAMIC ACID × 1 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.251
6Q0V Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 Deposited 2019-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded P7M N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.242
6Q0W Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39 Deposited 2019-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.264
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–395（395 aa）
Chain K 706–1140（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6SJ7 Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam Deposited 2019-08-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6UD7 Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam Deposited 2019-09-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded GOL GLYCEROL × 2 EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
Resolution 2.30 Å R-free 0.248
6UE5 Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzenesulfonamide Deposited 2019-09-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded Q5J 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.5 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic 676 dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
Resolution 2.61 Å R-free 0.266
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5
Resolution 3.58 Å R-free 0.267
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–1140（1140 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；100 mM Tri-Na citrate pH 5.5 18% PEG 1000
Resolution 3.09 Å R-free 0.279
6ZX9 Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
Resolution 2.52 Å R-free 0.260
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain A 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Chain I 1–1140（1140 aa）
Chain M 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7OO3 Pol II-CSB-CSA-DDB1-UVSSA (Structure1) Deposited 2021-05-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7OOB Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) Deposited 2021-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OOP Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3) Deposited 2021-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OPC Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4) Deposited 2021-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OPD Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) Deposited 2021-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7UKN Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 6.5-6.7), 16% PEG 4000, 50 mM NaCl, 5 mM DTT
Resolution 2.90 Å R-free 0.261
7V7B CryoEM structure of DDB1-VprBP complex in ARM-up conformation Deposited 2021-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Chain D 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7V7C CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex Deposited 2021-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Chain F 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7ZN7 Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD Deposited 2022-04-20 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–396（396 aa）
Chain A 706–1140（435 aa）
Mutation：delta396-705 GNGNSG Mutation：delta396-705 GNGNSG ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot
Resolution 3.78 Å
7ZNN Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and full-length rat STAT2 Deposited 2022-04-21 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–396（396 aa）
Chain A 706–1140（435 aa）
Mutation：Residues 396-705 have been replaced by a GNGNSG-linker Mutation：Residues 396-705 have been replaced by a GNGNSG-linker ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot
Resolution 4.80 Å
8AJM Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5 Deposited 2022-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
8AJN Structure of the human DDB1-DCAF12 complex Deposited 2022-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8AJO Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5 Deposited 2022-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 30.60 Å
8B3D Structure of the Pol II-TCR-ELOF1 complex. Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8B3F Pol II-CSB-CSA-DDB1-ELOF1 Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 16 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 13 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 6 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 3 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 1 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 2 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 2 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 3 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 4 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 3 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 1 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 15 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 14 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 16 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 15 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 3 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 3 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 4 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 11 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 15 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 13 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 10 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 11 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 22 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 24 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 3 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 6 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 8 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4? coldroom
Resolution 3.40 Å
8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.20 Å
8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7X Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.60 Å
8D81 Cereblon~DDB1 bound to Pomalidomide Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–395（395 aa） Fragment：residues 396 through 706 deleted, substituted with GNGNSG,residues 396 through 706 deleted, substituted with GNGNSG
Chain A 706–1140（435 aa） Fragment：residues 396 through 706 deleted, substituted with GNGNSG,residues 396 through 706 deleted, substituted with GNGNSG
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.90 Å
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8G46 Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Deposited 2023-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140
Chain A 706–1140（435 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140
Not recorded ZN ZINC ION × 1 YK3 tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP, 0.011% LMNG
cryo-EM vitrification conditions Cryogen ETHANE；detergent added directly before grid application
Resolution 2.20 Å
8G66 Structure with SJ3149 Deposited 2023-02-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.50 Å R-free 0.262
8OJH Crystal structure of human CRBN-DDB1 in complex with compound 4 Deposited 2023-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.72 Å R-free 0.254
8QH5 CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Deposited 2023-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8ROX Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 12 Deposited 2024-01-12 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded A1H17 5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-~{N},~{N},3-trimethyl-furan-2-carboxamide;ethane × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ROY Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24 Deposited 2024-01-12 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded A1H18 1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{N}-methyl-piperidine-4-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8T9A CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 Deposited 2023-06-23 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8TL6 Cryo-EM structure of DDB1deltaB-DDA1-DCAF5 Deposited 2023-07-26 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM HEPES, pH 7.4, 200mM NaCl, 4mM TCEP
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.63 Å
8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 3.30 Å
8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.41 Å
8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.50 Å
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded WO8 (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8WQR Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8ZSW Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex Deposited 2024-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1M MES (pH 6.5), 0.1M sodium acetate, 27%(w/v) PEG 400
Resolution 2.25 Å R-free 0.229
9BBE Co-crystal structure of human DDB1 bound to fragment UB028668 Deposited 2024-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1AK9 5-(4-methoxyphenyl)-3-[(3S)-pyrrolidin-3-yl]-1,2,4-oxadiazole × 1 UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 2.00 Å R-free 0.239
9BBG Co-crystal structure of human DDB1 bound to fragment UB028671 Deposited 2024-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1ALA 1H-indol-6-amine × 1 EDO 1,2-ETHANEDIOL × 6 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 1.70 Å R-free 0.218
9BBH Co-crystal structure of human DDB1 bound to fragment UB028670 Deposited 2024-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 VVP 4-methoxy-1H-indole × 2 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 2.00 Å R-free 0.232
9BBI Co-crystal structure of human DDB1 bound to fragment UB028669 Deposited 2024-04-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1ALB 3-([1,3]oxazolo[4,5-b]pyridin-2-yl)aniline × 1 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 1.90 Å R-free 0.221
9BJZ Structure of the human DDD-Ube2e2 complex Deposited 2024-04-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 replaced with GNGNSG Mutation：residues 396-705 replaced with GNGNSG No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9BZ0 Structure of an STK19-containing TC-NER complex Deposited 2024-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
9C5T Cryo EM structure of DCAF2 Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9C5U Cryo EM structure of DCAF2:Compound 1 complex Deposited 2024-06-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded A1AUM 1'-acetyl-1',4'-dihydro-3'H-spiro[cyclopentane-1,2'-quinoxalin]-3'-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9C5V Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded A1AUO N-({4-[(4-{[1'-(chloroacetyl)-3'-oxo-3',4'-dihydro-1'H-spiro[cyclopentane-1,2'-quinoxalin]-6'-yl]oxy}piperidin-1-yl)methyl]phenyl}methyl)-2-[(6S,10P)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9D0W Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 Deposited 2024-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9DHD The ternary complex of DDB1, DDA1, DET1 Deposited 2024-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–1140（1139 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Mutation：deletion of residues 396-705 Mutation：deletion of residues 396-705 ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9DWW Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 Deposited 2024-10-10 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain I 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain C 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain E 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain G 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain K 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain M 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain O 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9EJQ Crystal structure of DDB1 in complex with XS381952 Deposited 2024-11-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 GOL GLYCEROL × 6 A1BIX (4S)-4-(3-ethoxyphenyl)-3-methyl-1-[(4R)-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 7 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.0 P3350, 0.2 di-NH4tart
Resolution 1.87 Å R-free 0.220
9ER2 PolII-TCR-STK19 structure. Deposited 2024-03-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9FD2 Structure of Pol II-TC-NER-STK19 complex Deposited 2024-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain b 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9FJX Crystal structure of human CRBN-DDB1 in complex with Lenalidomide Deposited 2024-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.00 Å R-free 0.232
9FMR Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835 Deposited 2024-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–391（391 aa）
Chain A 708–1140（433 aa）
Chain D 1–391（391 aa）
Chain D 708–1140（433 aa）
Chain G 1–391（391 aa）
Chain G 708–1140（433 aa）
Not recorded RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；1 M potassium citrate and 15% glycerol
Resolution 3.90 Å R-free 0.250
9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Mutation：aa396-705 replaced with GNGNSG ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 2.93 Å
9HPJ Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2 Deposited 2024-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Mutation：aa396-705 replaced with GNGNSG ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 3.10 Å
9HWG Structure of the transcribing Pol II-TCR-RECQL5 complex Deposited 2025-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9IVD Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1 Deposited 2024-07-23 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9J6J HBx fused DDB1 4M mutant Deposited 2024-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Mutation：A583D,W774K,I770D,R772E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9J6K HBx complexed with DDB1 Deposited 2024-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
9LTJ Cryo-EM structure of DDB1-DDA1-DET1 complex Deposited 2025-02-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9LTL Cryo-EM structure of DDB1-DDA1-DET1 complex Deposited 2025-02-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9LTO Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9LTR Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex Deposited 2025-02-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9LTW protein structure of DDB1-DDA1-DET1 Deposited 2025-02-06 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9LTZ protein structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9LU1 protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9LUL Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1) Deposited 2025-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain c 1–1140（1140 aa）
Chain f 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.99 Å
9LWI The head region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9LWJ The head-arm region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.19 Å
9LWL HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.25 Å
9M0Y Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2) Deposited 2025-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain S 1–1140（1140 aa）
Chain V 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
Resolution 3.25 Å R-free 0.261
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
Resolution 3.40 Å R-free 0.271
9NGT Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR Deposited 2025-02-22 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
Resolution 2.95 Å R-free 0.260
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–393（393 aa）
Chain A 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350
Resolution 2.93 Å R-free 0.278
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded A1B7G N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–391（391 aa）
Chain A 710–1140（431 aa）
Not recorded ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission Deposited 2025-05-28 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–381（381 aa） Fragment：UNP residues 1-381,706-1140
Chain A 706–1140（435 aa） Fragment：UNP residues 1-381,706-1140
Not recorded A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350
Resolution 3.41 Å R-free 0.252
9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–395（395 aa） Fragment：UNP residues 1-395,706-1140
Chain C 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 sec blot force 4
Resolution 2.94 Å
9S3R Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB Deposited 2025-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1JLV 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-enyl]pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Applied 3.5 uL of sample to grid. wait = 10 sec, drain = 0 sec, blot = 4 sec, blotForce = 4
Resolution 3.30 Å
9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
Resolution 2.39 Å R-free 0.244
9U7T Structure of the human DCAF8-DDB1 complex Deposited 2025-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9UWG Structure of the human DCAF2-DDB1 complex Deposited 2025-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.54 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9W2F Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR Deposited 2025-07-27 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1EUN (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9W90 DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex Deposited 2025-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9ZXM DDB1 delta with compound 6 Deposited 2026-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Chain A 706–1140（435 aa）
Not recorded A1C4E (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-3-[(propan-2-yl)oxy]benzene-1-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350
Resolution 2.19 Å R-free 0.246
9ZXN DDB1 delta with compound 26 Deposited 2026-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Chain A 706–1140（435 aa）
Not recorded A1C4F (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-1-methyl-5-[(propan-2-yl)oxy]-1H-1,3-benzimidazole-7-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350
Resolution 2.07 Å R-free 0.235

202 other PDB entries and 290 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 29–423； UniProt 1–395 Author chain A； PDBConstruct 430–864； UniProt 706–1140

Protein cereblon

Homo sapiens

UniProt Q96SW2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–441 Not recorded DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 （Q16531） Bromodomain-containing protein 4 × 1 （O60885） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8) Resolution 4.38 Å R-free 0.301

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BN9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 40–442（403 aa）
Chain E 40–442（403 aa）
Not recorded A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
11MR Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement) Deposited 2026-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Chain D 40–442（403 aa）
Not recorded ZN ZINC ION × 2 A1C9W N-[(3S)-2,6-dioxopiperidin-3-yl]-2-fluoro-3-[(2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}propan-2-yl)carbamamido]benzamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES (pH 7.5), 240 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
4M91 crystal structure of hN33/Tusc3-peptide 1 Deposited 2013-08-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 229–240（12 aa） Fragment：unp residues 229-240
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；0.2 M KSCN, 10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Resolution 1.10 Å R-free 0.160
4TZ4 Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide Deposited 2014-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 47–427（381 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K
Resolution 3.01 Å R-free 0.271
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 39–441（403 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 39–441（403 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 40–442（403 aa） Fragment：residues 40-442
Not recorded 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200mM NaCl, 20% PEG 3350
Resolution 3.20 Å R-free 0.267
6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.99 Å R-free 0.333
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
Resolution 6.34 Å R-free 0.381
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 3.33 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5
Resolution 3.58 Å R-free 0.267
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 40–442（403 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
7BQU Cereblon in complex with SALL4 and (S)-thalidomide Deposited 2020-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa）
Not recorded EF2 S-Thalidomide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride
Resolution 1.90 Å R-free 0.236
7BQV Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide Deposited 2020-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa）
Mutation：C366S F4U 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG 4000, 0.1 M MES (pH 6.0), 0.2 M lithium sulfate
Resolution 1.80 Å R-free 0.223
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 40–442（403 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 40–442（403 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4? coldroom
Resolution 3.40 Å
8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.20 Å
8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7X Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.60 Å
8D81 Cereblon~DDB1 bound to Pomalidomide Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.90 Å
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8G66 Structure with SJ3149 Deposited 2023-02-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.50 Å R-free 0.262
8OJH Crystal structure of human CRBN-DDB1 in complex with compound 4 Deposited 2023-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.72 Å R-free 0.254
8RQ1 Crystal structure of CRBN-midi Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium citrate, 20% (w/v) PEG 3350, and 0.1 M BIS-TRIS propane pH 6.5
Resolution 3.11 Å R-free 0.300
8RQ8 Crystal structure of CRBN-midi in complex with mezigdomide Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；214 uM mezigdomide 0.2 M sodium acetate, 25% (w/v) PEG 3350, and 0.1 M BIS-TRIS pH 6.5
Resolution 2.19 Å R-free 0.285
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RQA Crystal structure of CRBN-midi in complex with Lenalidomide Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded LVY S-Lenalidomide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris pH 8, 20 % w/v PEG 4000, 1.2 % myo-inositol
Resolution 2.50 Å R-free 0.342
8RQC Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2 Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Chain D 41–187（147 aa）
Chain D 249–426（178 aa）
Not recorded ZN ZINC ION × 4 QFC Mezigdomide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulphate, 25% (w/v) PEG 3350, and 0.1 M HEPES pH 7.5
Resolution 2.15 Å R-free 0.286
8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 3.30 Å
8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.41 Å
8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.50 Å
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.95 Å R-free 0.272
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.95 Å R-free 0.272
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded WO8 (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 319–427（109 aa）
Chain B 319–427（109 aa）
Chain C 319–427（109 aa）
Not recorded ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
Resolution 1.60 Å R-free 0.205
9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 319–427（109 aa）
Chain E 319–427（109 aa）
Chain F 319–427（109 aa）
Not recorded ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
Resolution 1.60 Å R-free 0.205
9D0W Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9D0X Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 (local mask) Deposited 2024-08-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9DUR Cryo-EM Structure of CRBN:dHTC1:ENL YEATS Deposited 2024-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；30 mM HEPES/NaOH pH7.4, 150 mM NaCl. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C
Resolution 2.90 Å
9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9DWW Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 Deposited 2024-10-10 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain N 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9FJX Crystal structure of human CRBN-DDB1 in complex with Lenalidomide Deposited 2024-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.00 Å R-free 0.232
9GAO Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide Deposited 2024-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1IJM 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Buffer system I (Molecular Dimensions), 15.45% v/v Precipitant mix 2 (MD), 180 mM Monosaccharides (MD)
Resolution 1.95 Å R-free 0.286
9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
Resolution 2.50 Å R-free 0.303
9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
Resolution 2.50 Å R-free 0.303
9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Chain C 41–442（402 aa）
Not recorded ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 2.93 Å
9HPJ Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2 Deposited 2024-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Chain C 41–442（402 aa）
Not recorded ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 3.10 Å
9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
Resolution 3.25 Å R-free 0.261
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
Resolution 3.40 Å R-free 0.271
9NGT Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR Deposited 2025-02-22 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
Resolution 2.95 Å R-free 0.260
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350
Resolution 2.93 Å R-free 0.278
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Not recorded A1B7G N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 47–424（378 aa）
Not recorded ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 46–427（382 aa）
Not recorded ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–427（427 aa）
Not recorded ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9Q03 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined) Deposited 2025-08-12 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1CM7 (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350
Resolution 3.41 Å R-free 0.252
9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 sec blot force 4
Resolution 2.94 Å
9Q33 Cereblon Ternary Complex with Blimp1 and compound 5 Deposited 2025-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1CN1 N-({(4R)-7-[(1S)-2-amino-1-(4-bromo-2-methylphenyl)-2-oxoethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyrazin-3-yl}methyl)-13-{4-[(3R)-2,6-dioxopiperidin-3-yl]anilino}tridecanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.20 Å
9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 46–427（382 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
Resolution 2.39 Å R-free 0.244
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.54 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9W2F Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR Deposited 2025-07-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 45–425（381 aa）
Not recorded ZN ZINC ION × 1 A1EUN (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Y7D Cereblon with Golcadomide and Ikaros ZF1-2-3 Deposited 2025-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 2 A1AF4 Golcadomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.26 Å
9YA9 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) Deposited 2025-09-15 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded A1CTU (3R)-3-(6-{[(3R,4R)-1-{5-chloro-4-[(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrimidin-2-yl}-3-methylpiperidin-4-yl]amino}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å

93 other PDB entries and 141 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRBN_HUMAN
Isoform Q96SW2-2
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 23–463； UniProt 1–441

Bromodomain-containing protein 4

Homo sapiens

UniProt O60885

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 42–168 Fragment：residues 42-168 Mutation：T43M DNA damage-binding protein 1,DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8) Resolution 4.38 Å R-free 0.301

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6BN9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2I8N Solution structure of the second bromodomain of Brd4 Deposited 2006-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：C-terminal bromodomain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；293 K；Ionic strength (raw mmCIF value) 20mM Na2HPO4, 50mM NaCl；Pressure 1
NMR sample composition 1.0mM 15N, 13C-labeled BRD4 C-terminal domain, 20mM phosphate buffer(pH6.0), 50mM NaCl, 5mM EDTA, 10%(v/v)D2O | 90% H2O/10% D2O
Resolution not provided
2LSP solution structures of BRD4 second bromodomain with NF-kB-K310ac peptide Deposited 2012-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 333–460（128 aa） Fragment：second bromodomain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2MJV Solution structures of second bromodomain of Brd4 with di-acetylated Twist peptide Deposited 2014-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 333–460（128 aa） Fragment：bromodomain 2 (UNP residues 333-460)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 5 mM [U-100% 2H] DTT, 100 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N3K Human Brd4 ET domain in complex with MLV Integrase C-term Deposited 2015-06-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 600–678（79 aa） Fragment：Brd4 ET domain (UNP residues 600-678)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.25；Pressure ambient
NMR sample composition 0.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 100% D2O | 100% D2O
NMR sample composition 0.4-0.8 mM [U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.4-0.8 mM [U-99% 15N] Brd4 ET, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM MLV IN EBM, 0.5 mM DSS, 0.002 v/v sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NCZ Solution NMR structures of BRD4 ET domain in complex with NSD3_1 peptide Deposited 2016-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 601–683（83 aa） Fragment：residues 601-683
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2ND0 Solution NMR structures of BRD4 ET domain with LANA peptide Deposited 2016-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 601–683（83 aa） Fragment：residues 601-683
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2ND1 Solution NMR structures of BRD4 ET domain in complex with NSD3_3 peptide Deposited 2016-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 601–683（83 aa） Fragment：residues 601-683
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure ambient
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NNU Crystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4 Deposited 2006-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1343–1362（20 aa） Fragment：C-terminal residues (1343-1362)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100mM citrate, 1.8-2.0M Na-acetate, 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.59 Å R-free 0.233
2NNU Crystal Structure of the Papillomavirus DNA Tethering Complex E2:Brd4 Deposited 2006-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1343–1362（20 aa） Fragment：C-terminal residues (1343-1362)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；100mM citrate, 1.8-2.0M Na-acetate, 10mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.59 Å R-free 0.233
2OSS Crystal structure of the Bromo domain 1 in human Bromodomain Containing Protein 4 (BRD4) Deposited 2007-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo domain 1
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaNO3, 20% PEG3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.35 Å R-free 0.174
2OUO Crystal Structure of the Bromo domain 2 in human Bromodomain Containing Protein 4 (BRD4) Deposited 2007-02-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa） Fragment：Bromo domain 2
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M MIB, 30% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.89 Å R-free 0.216
2YEL Crystal Structure of the First Bromodomain of Human Brd4 with the inhibitor GW841819X Deposited 2011-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 WSH BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；17.5% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS TRIS PH 5.5.
Resolution 1.65 Å R-free 0.211
2YEM Crystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X Deposited 2011-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa） Fragment：C-TERMINAL BROMODOMAIN, RESIDUES 333-460
Not recorded WSH BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；2.5 M (NH4)2SO4, 0.1 M TRIS PH 8.5.
Resolution 2.30 Å R-free 0.229
2YEM Crystal Structure of the Second Bromodomain of Human Brd4 with the inhibitor GW841819X Deposited 2011-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 333–460（128 aa） Fragment：C-TERMINAL BROMODOMAIN, RESIDUES 333-460
Not recorded WSH BENZYL [(4R)-1-METHYL-6-PHENYL-4H-[1,2,4]TRIAZOLO[4,3-A][1,4]BENZODIAZEPIN-4-YL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；2.5 M (NH4)2SO4, 0.1 M TRIS PH 8.5.
Resolution 2.30 Å R-free 0.229
3MXF Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JQ1 Deposited 2010-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded JQ1 (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium × 1 IOD IODIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M NaI 0.1M BTProp pH 8.5 20% PEG3350 10% EtGhly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.184
3P5O Crystal Structure of the First Bromodomain of Human Brd4 in complex with IBET inhibitor Deposited 2010-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：BROMO DOMAIN 1, UNP residues 44-168
Not recorded EAM 2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M NaNO3, 20% PEG 3350, 10% ethylene glycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.60 Å R-free 0.185
3SVF Crystal Structure of the first bromodomain of human BRD4 in complex with a dihydro-quinazolin ligand Deposited 2011-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded WDR (4S)-6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-(2-hydroxyethoxy)-3-methyl-3,4-dihydroquinazolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M Na(OAc), 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.98 Å R-free 0.227
3SVG Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2011-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 ODR (1R)-1-[3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-ethoxyphenyl]ethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M Na2SO4, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.68 Å R-free 0.215
3U5J Crystal Structure of the first bromodomain of human BRD4 in complex with Alprazolam Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 08H 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2M Na2SO4, 0.1M BTProp pH 6.5, 20% PEG3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.177
3U5K Crystal Structure of the first bromodomain of human BRD4 in complex with Midazolam Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 08J 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M MES pH 5.5, 0.1M MgCl, 15% PEG 6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.260
3U5K Crystal Structure of the first bromodomain of human BRD4 in complex with Midazolam Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa）
Not recorded 08J 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M MES pH 5.5, 0.1M MgCl, 15% PEG 6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.260
3U5K Crystal Structure of the first bromodomain of human BRD4 in complex with Midazolam Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 42–168（127 aa）
Not recorded 08J 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M MES pH 5.5, 0.1M MgCl, 15% PEG 6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.260
3U5K Crystal Structure of the first bromodomain of human BRD4 in complex with Midazolam Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 42–168（127 aa）
Not recorded 08J 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M MES pH 5.5, 0.1M MgCl, 15% PEG 6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.80 Å R-free 0.260
3U5L Crystal Structure of the first bromodomain of human BRD4 in complex with a benzo-triazepine ligand (BzT-7) Deposited 2011-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 08K 8-chloro-1,4-dimethyl-6-phenyl-4H-[1,2,4]triazolo[4,3-a][1,3,4]benzotriazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M Na(malonate), 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.39 Å R-free 0.142
3UVW Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；278 K；0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0
Resolution 1.37 Å R-free 0.171
3UVX Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K12acK16ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；278 K；0.35M NaFortmate 20% PEG 3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 1.91 Å R-free 0.219
3UVY Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac) Deposited 2011-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Resolution 2.02 Å R-free 0.258
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa） Fragment：unp resideus 44-168
Chain C 42–168（127 aa） Fragment：unp resideus 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3UW9 Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac) Deposited 2011-12-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 42–168（127 aa） Fragment：unp resideus 44-168
Chain D 42–168（127 aa） Fragment：unp resideus 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0
Resolution 2.30 Å R-free 0.257
3ZYU Crystal Structure of the first bromodomain of human BRD4 in complex with I-BET151(GSK1210151A) Deposited 2011-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN (BD1), RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 4 1GH 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.201
3ZYU Crystal Structure of the first bromodomain of human BRD4 in complex with I-BET151(GSK1210151A) Deposited 2011-08-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN (BD1), RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 1GH 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.201
4A9L N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-DIMETHYL-6-(MORPHOLINE- 4-SULFONYL)-1,2,3,4-TETRAHYDROQUINAZOLIN-2-ONE Deposited 2011-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 P9L 1,3-dimethyl-6-(morpholin-4-ylsulfonyl)-3,4-dihydroquinazolin-2(1H)-one × 1 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20-30% PEG 3350, 0.2 M NACL, 0.1 HEPES PH 8.5, 10% ETHYLGLYCOL.
Resolution 1.60 Å R-free 0.206
4BJX N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK1324726A (I-BET726) Deposited 2013-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded 73B 4-[(2S,4R)-1-acetyl-4-[(4-chlorophenyl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；293 K；20% PEG3350, 0.2M NAK,TARTRATE, 0.1M BISTRISPROPANE PH 6.5, 20C
Resolution 1.59 Å R-free 0.185
4BW1 The first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand Deposited 2013-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded EDO 1,2-ETHANEDIOL × 3 S5B 4-[(2-tert-butylphenyl)amino]-7-(3,5-dimethyl-1,2-oxazol-4-yl)quinoline-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；25% PEG1500, 0.1M SPG BUFFER PH6.0
Resolution 1.40 Å R-free 0.208
4BW2 The first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand Deposited 2013-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded EDO 1,2-ETHANEDIOL × 1 UTH 4-((2-(TERT-BUTYL)PHENYL)AMINO)-7-(3,5-dimethylisoxazol-4-yl)-1,8-naphthyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.1M MES PH8.6, 20% PEG6000, 0.2M MGCL2, pH 6.0
Resolution 1.92 Å R-free 0.222
4BW3 The first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand Deposited 2013-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 9BM 4-((2-(tert-butyl)phenyl)amino)-7-(3,5-dimethylisoxazol-4-yl)-6-methoxy-1,5-naphthyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；20% PEG3350, 0.2M NANO3, 0.1M BIS-TRIS-PROPANE PH8.5
Resolution 1.50 Å R-free 0.231
4BW4 The first bromodomain of human BRD4 in complex with 3,5 dimethylisoxaxole ligand Deposited 2013-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded 9B6 7-(3,5-dimethylisoxazol-4-yl)-8-methoxy-1-(2-(trifluoromethoxy)phenyl)-1h-imidazo[4,5-c][1,5]naphthyridin-2(3h)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1M TRIS PH8.0, 25% PE6000, 0.2M MGCL2
Resolution 1.67 Å R-free 0.220
4C66 Discovery of Epigenetic Regulator I-BET762: Lead Optimization to Afford a Clinical Candidate Inhibitor of the BET Bromodomains Deposited 2013-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-167
Not recorded H4C 4-(2-chlorophenyl)-2-ethyl-9-methyl-6,8-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 1M LICL, 0.1M NAAC (UNBUFFERED), 30% PEG6000
Resolution 1.87 Å R-free 0.266
4C67 Discovery of Epigenetic Regulator I-BET762: Lead Optimization to Afford a Clinical Candidate Inhibitor of the BET Bromodomains Deposited 2013-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded L5S 13-methyl-7-phenyl-3-thia-1,8,11,12-tetraazatricyclo trideca-2(6),4,7,10,12-pentaene × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.2M CACL2, 0.1M MES PH6.5, 20% PEG6000
Resolution 1.55 Å R-free 0.186
4CL9 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH I-BET295 Deposited 2014-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 IES propan-2-yl N-[(2S,4R)-1-ethanoyl-2-methyl-6-[4-[[8-(oxidanylamino)-8-oxidanylidene-octanoyl]amino]phenyl]-3,4-dihydro-2H-quinolin-4-yl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 25% PEG6000, 0.1M TRISHCL PH 8.0, 0.2M LICL
Resolution 1.40 Å R-free 0.199
4CLB N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH IBET-295 Deposited 2014-01-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 83T propan-2-yl N-[(2S,4R)-1-ethanoyl-2-methyl-6-[4-(methylaminomethyl)phenyl]-3,4-dihydro-2H-quinolin-4-yl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M BTP PH 8.5, 20% PEG3350, 0.2M NAF
Resolution 1.60 Å R-free 0.205
4DON Brd4 Bromodomain 1 complex with a fragment 3,4-Dihydro-3-methyl-2(1H)-quinazolinon Deposited 2012-02-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：Bromo 1 domain, UNP residues 44-166
Not recorded 3PF 3-methyl-3,4-dihydroquinazolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.52 Å R-free 0.218
4E96 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor PFi-1 Deposited 2012-03-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 0NS 2-methoxy-N-(3-methyl-2-oxo-1,2,3,4-tetrahydroquinazolin-6-yl)benzenesulfonamide × 1 NA SODIUM ION × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M Na(malonate) 0.1M BTProp pH 8.5 20% PEG3350 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.92 Å R-free 0.285
4F3I Crystal structure of the first bromodomain of human BRD4 in complex with MS417 inhibitor Deposited 2012-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 2 0S6 methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；25% PEG3350, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.40 Å R-free 0.183
4GPJ Crystal Structure of the first bromodomain of human BRD4 in complex with a isoxazolylbenzimidazole ligand Deposited 2012-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 0Q1 (1R)-6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-phenyl-2,3-dihydro-1H-inden-1-ol × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.20M Na2SO4, 0.1M BTProp, 20.0% PEG 3350, 10.0% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.204
4HBV Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolin ligand Deposited 2012-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 15E 6-bromo-3-methyl-3,4-dihydroquinazolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2M NaNO3, 0.1M BTProp pH 6.5, 20% PEG3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.63 Å R-free 0.241
4HBW Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazoline ligand Deposited 2012-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 14Z N-ethyl-3-methyl-2-oxo-1,2,3,4-tetrahydroquinazoline-6-sulfonamide × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20M K3(cit), 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.69 Å R-free 0.228
4HBX Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolin ligand Deposited 2012-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 14X 3-methyl-6-(pyrrolidin-1-ylsulfonyl)-3,4-dihydroquinazolin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M KSCN, 0.1M BTProp pH 7.5, 20% PEG3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.62 Å R-free 0.210
4HBY Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolin ligand Deposited 2012-09-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 13F 3-methyl-2-oxo-N-phenyl-1,2,3,4-tetrahydroquinazoline-6-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M KSCN, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.59 Å R-free 0.239
4HXK Brd4 Bromodomain 1 complex with 6,7-DIHYDROTHIENO[3,2-C]PYRIDIN-5(4H)-YL(1H-IMIDAZOL-1-YL)METHANONE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 1AJ 6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl(1H-imidazol-1-yl)methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.61 Å R-free 0.203
4HXL Brd4 Bromodomain 1 complex with 3-CYCLOHEXYL-N-{3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)-5-[(THIOPHEN-2-YLSULFONYL)AMINO]PHENYL}PROPANAMIDE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 1A9 3-cyclohexyl-N-{3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)-5-[(thiophen-2-ylsulfonyl)amino]phenyl}propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.52 Å R-free 0.191
4HXM Brd4 Bromodomain 1 complex with N-{3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)-5-[(THIOPHEN-2-YLSULFONYL)AMINO]PHENYL}BUTANAMIDE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded 1A8 N-{3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)-5-[(thiophen-2-ylsulfonyl)amino]phenyl}butanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.50 Å R-free 0.215
4HXN Brd4 Bromodomain 1 complex with 4-(2-FLUOROPHENYL)-1,3-THIAZOL-2(3H)-ONE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 1A7 4-(2-fluorophenyl)-1,3-thiazol-2(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.49 Å R-free 0.213
4HXO Brd4 Bromodomain 1 complex with 3-{[(3-METHYL-1,2-OXAZOL-5-YL)METHYL]SULFANYL}[1,2,4]TRIAZOLO[4,3-A]PYRIDINE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 1A6 3-{[(3-methyl-1,2-oxazol-5-yl)methyl]sulfanyl}[1,2,4]triazolo[4,3-a]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.76 Å R-free 0.229
4HXP Brd4 Bromodomain 1 complex with 4-(2-OXO-1,3-OXAZOLIDIN-3-YL)BENZAMIDE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded 1A5 4-(2-oxo-1,3-oxazolidin-3-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.73 Å R-free 0.193
4HXR Brd4 Bromodomain 1 complex with N-[3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)PHENYL]THIOPHENE-2-SULFONAMIDE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 1A4 N-[3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)phenyl]thiophene-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.53 Å R-free 0.199
4HXS Brd4 Bromodomain 1 complex with N-[3-(2-OXO-2,3-DIHYDRO-1,3-THIAZOL-4-YL)PHENYL]-1-PHENYLMETHANESULFONAMIDE inhibitor Deposited 2012-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded 1A3 N-[3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)phenyl]-1-phenylmethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Na formate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.43 Å R-free 0.204
4IOO Crystal Structure of the first bromodomain of BRD4 in complex with N-methyltrimethylacetamide Deposited 2013-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first bromodomain (unp residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 5 BAE N-methyltrimethylacetamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol, pH 7.5, vapor diffusion, temperature 277K
Resolution 1.25 Å R-free 0.167
4IOQ Crystal Structure of the first bromodomain of BRD4 in complex with pyrrolidin-2-one Deposited 2013-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded BAQ pyrrolidin-2-one × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol , pH 7.5, VAPOR DIFFUSION, temperature 277K
Resolution 1.50 Å R-free 0.194
4IOR Crystal Structure of the first bromodomain of BRD4 in complex with DMSO Deposited 2013-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first bromodomain (unp residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol, pH 7.5, vapor diffusion, temperature 277K
Resolution 1.40 Å R-free 0.191
4J0R Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2013-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 4 1H2 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(R)-hydroxy(phenyl)methyl]phenol × 1 IOD IODIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M NaI, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.72 Å R-free 0.220
4J0S Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2013-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 4 1H3 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(S)-hydroxy(phenyl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M Na/KPO4, 20% PEG 3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.84 Å R-free 0.226
4J3I X-ray crystal structure of bromodomain complex to 1.24 A resolution Deposited 2013-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 1K0 2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% (W/V) PEG 3350, 0.1 M BIS-TRIS, 0.2 M LITHIUM SULFATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.24 Å R-free 0.145
4KV1 Crystal Structure of Brd4 Bromodomain 1 in Complex with Acetylated Rel Peptide Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 41–168（128 aa） Fragment：UNP residues 41-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；20% PEG 3350, 0.2 M NaNO3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 1.50 Å R-free 0.222
4KV1 Crystal Structure of Brd4 Bromodomain 1 in Complex with Acetylated Rel Peptide Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 41–168（128 aa） Fragment：UNP residues 41-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；20% PEG 3350, 0.2 M NaNO3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 1.50 Å R-free 0.222
4KV4 Brd4 Bromodomain 2 in Complex with Acetylated Rel Peptide Deposited 2013-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 351–459（109 aa） Fragment：UNP residues 351-459
Not recorded DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；2.5 M (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.00 Å R-free 0.258
4LR6 Structure of BRD4 bromodomain 1 with a 3-methyl-4-phenylisoxazol-5-amine fragment Deposited 2013-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：bromodomain 1 (UNP residues 42-168)
Not recorded FMT FORMIC ACID × 2 1XA 3-methyl-4-phenyl-1,2-oxazol-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；278 K；3.682 M Formate, 10% Glycerol, 0.1 M Tris-HCl pH 8.5, vapor diffusion, sitting drop, temperature 278K
Resolution 1.29 Å R-free 0.242
4LRG Structure of BRD4 bromodomain 1 with a dimethyl thiophene isoxazole azepine carboxamide Deposited 2013-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：bromodomain 1 (UNP residues 42-168)
Not recorded 1XB 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-[1,2]oxazolo[5,4-c]thieno[2,3-e]azepin-6-yl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；0.1M Bis-Tris pH 7.0, 150mM NaCl, 25% PEG3350. Cryo used: 23% Glycerol in well solution, temperature 278K, VAPOR DIFFUSION, SITTING DROP
Resolution 2.21 Å R-free 0.288
4LYI Crystal Structure of apo-BRD4(1) Deposited 2013-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first bromodomain domain (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 10 IOD IODIDE ION × 1 NA SODIUM ION × 1 21H oxydimethanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；293 K；bis tris propane, PEG 3350, NaI, ethylene glycol, pH 8.3, vapor diffusion, temperature 293K
Resolution 1.30 Å R-free 0.198
4LYS Crystal Structure of BRD4(1) bound to Colchiceine Deposited 2013-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Not recorded NA SODIUM ION × 2 2SJ N-[(7S)-10-hydroxy-1,2,3-trimethoxy-9-oxo-5,6,7,9-tetrahydrobenzo[a]heptalen-7-yl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；bis tris, PEG 3350, NaCl, pH 6.5, vapor diffusion, temperature 293K
Resolution 1.83 Å R-free 0.267
4LYW Crystal Structure of BRD4(1) bound to inhibitor XD14 Deposited 2013-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Not recorded 21Q 4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；NaFormate, pH 7.5, vapor diffusion, temperature 293K
Resolution 1.95 Å R-free 0.235
4LZR Crystal Structure of BRD4(1) bound to Colchicine Deposited 2013-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Not recorded LOC N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293 K；1.4 M Na-K-phosphate, pH 8.2, VAPOR DIFFUSION, temperature 293K
Resolution 1.85 Å R-free 0.243
4LZS Crystal Structure of BRD4(1) bound to inhibitor XD46 Deposited 2013-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Not recorded L46 4-acetyl-3-ethyl-N,5-dimethyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；NaCitrate, PEG 3,350, pH 7.5, vapor diffusion, temperature 293K
Resolution 2.20 Å R-free 0.242
4MEN Crystal Structure of the first bromodomain of human BRD4 in complex with a 5-methyl-triazolopyrimidine ligand Deposited 2013-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 25K N,5-dimethyl-N-(4-methylbenzyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20M Na(malonate), 0.1M BTProp, 20.0% PEG 3350 10.0% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.81 Å R-free 0.219
4MEO Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-methyl-quinoline ligand Deposited 2013-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 25V N-[3-(2-methyl-1-oxidoquinolin-4-yl)phenyl]acetamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.20M LiCl, 0.1M TRIS, 20.0% PEG 6K, 10.0% EtGly, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.72 Å R-free 0.213
4MEP Crystal Structure of the first bromodomain of human BRD4 in complex with a 3-chloro-pyridone ligand Deposited 2013-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded 24Y 3-chloro-5-[1-(3-methylpyridin-2-yl)-3-phenyl-1H-1,2,4-triazol-5-yl]pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.20M NaBr, 0.1M BTProp, 20.0% PEG 3350, 10.0% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.85 Å R-free 0.235
4MEQ Crystal Structure of the first bromodomain of human BRD4 in complex with a 5-methyl-triazolopyrimidine ligand Deposited 2013-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 25O 5-methyl-7-phenyl[1,2,4]triazolo[1,5-a]pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M Na2SO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.77 Å R-free 0.223
4MR3 Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolinone ligand (RVX-OH) Deposited 2013-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 1K0 2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M NaBr, 0.1M BTProp, 20.0% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.68 Å R-free 0.185
4MR4 Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazolinone ligand (RVX-208) Deposited 2013-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 1K0 2-[4-(2-hydroxyethoxy)-3,5-dimethylphenyl]-5,7-dimethoxyquinazolin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M Na2SO4, 20% PEG3350 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.66 Å R-free 0.194
4NQM Crystal Structure of the first bromodomain of human BRD4 in complex with a triazolo-phthalazine ligand Deposited 2013-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded Y1Z 2-chloro-N-[5-(3-methyl[1,2,4]triazolo[3,4-a]phthalazin-6-yl)-2-(morpholin-4-yl)phenyl]benzenesulfonamide × 1 SIN SUCCINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.1M SPG pH 8.0, 60.0% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.58 Å R-free 0.203
4NR8 Crystal structure of the first bromodomain of human BRD4 in complex with an isoxazolyl-benzimidazole ligand Deposited 2013-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded K POTASSIUM ION × 1 2LL 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazole × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M NaI, 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.64 Å R-free 0.246
4NUC Crystal structure of the first bromodomain of human BRD4 in complex with MS435 inhibitor Deposited 2013-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain, residues 44-168
Not recorded 435 4-[(E)-(4-hydroxy-3,5-dimethylphenyl)diazenyl]-N-(pyridin-2-yl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；30% PEG 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Magnesium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.40 Å R-free 0.186
4NUD Crystal structure of the first bromodomain of human BRD4 in complex with MS436 inhibitor Deposited 2013-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain, residues 44-168
Not recorded NUD 4-[(E)-(2-amino-4-hydroxy-5-methylphenyl)diazenyl]-N-(pyridin-2-yl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；30% PEG 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Magnesium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.20 Å R-free 0.171
4NUE Crystal structure of the first bromodomain of human BRD4 in complex with MS267 inhibitor Deposited 2013-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain, residues 44-168
Not recorded NUE 4-[(E)-(2-amino-4-hydroxy-3,5-dimethylphenyl)diazenyl]-N-(pyridin-2-yl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；14% PEG 4,000, 0.2MgCl2, 0.1M Tris pH 8.5, 15% ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.30 Å R-free 0.188
4O70 Crystal structure of the first bromodomain of human BRD4 in complex with DINACICLIB Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM DINACICLIB, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.234
4O70 Crystal structure of the first bromodomain of human BRD4 in complex with DINACICLIB Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM DINACICLIB, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.234
4O71 Crystal structure of the first bromodomain of human BRD4 in complex with FLAVOPIRIDOL Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded CPB 2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM FLAVOPIRIDOL, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.36 Å R-free 0.162
4O71 Crystal structure of the first bromodomain of human BRD4 in complex with FLAVOPIRIDOL Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded CPB 2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM FLAVOPIRIDOL, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.36 Å R-free 0.162
4O72 Crystal structure of the first bromodomain of human BRD4 in complex with NU7441 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2R4 8-(dibenzo[b,d]thiophen-4-yl)-2-(morpholin-4-yl)-4H-chromen-4-one × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM NU7441, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.156
4O74 Crystal structure of the first bromodomain of human BRD4 in complex with BI 2536 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM BI2536, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.45 Å R-free 0.178
4O74 Crystal structure of the first bromodomain of human BRD4 in complex with BI 2536 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM BI2536, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.45 Å R-free 0.178
4O75 Crystal structure of the first bromodomain of human BRD4 in complex with FOSTAMATINIB Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RC [6-({5-fluoro-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}amino)-2,2-dimethyl-3-oxo-2,3-dihydro-4H-pyrido[3,2-b][1,4]oxazin-4-yl]methyl dihydrogen phosphate × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM FOSTAMATINIB, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.199
4O76 Crystal structure of the first bromodomain of human BRD4 in complex with TG101209 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101209, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.171
4O76 Crystal structure of the first bromodomain of human BRD4 in complex with TG101209 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101209, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.171
4O76 Crystal structure of the first bromodomain of human BRD4 in complex with TG101209 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101209, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.171
4O76 Crystal structure of the first bromodomain of human BRD4 in complex with TG101209 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 1M3 N-tert-butyl-3-[(5-methyl-2-{[4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101209, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.171
4O77 Crystal structure of the first bromodomain of human BRD4 in complex with SB 202190 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RE 4-[4-(4-fluorophenyl)-5-(pyridin-4-yl)-1H-imidazol-2-yl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB 202190, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.207
4O77 Crystal structure of the first bromodomain of human BRD4 in complex with SB 202190 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RE 4-[4-(4-fluorophenyl)-5-(pyridin-4-yl)-1H-imidazol-2-yl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB 202190, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.00 Å R-free 0.207
4O78 Crystal structure of the first bromodomain of human BRD4 in complex with GW612286X Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded SAV N~4~-(3-methyl-1H-indazol-6-yl)-N~2~-(3,4,5-trimethoxyphenyl)pyrimidine-2,4-diamine × 1 EDO 1,2-ETHANEDIOL × 5 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM GW612286X, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.34 Å R-free 0.144
4O7A Crystal structure of the first bromodomain of human BRD4 in complex with SB-409514 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RF 3-[(3-chloro-4-hydroxyphenyl)amino]-4-(3-chlorophenyl)-1H-pyrrole-2,5-dione × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB-409514, HANGING DROP, VAPOR-DIFFUSION, TEMPERATURE 291K
Resolution 1.34 Å R-free 0.174
4O7B Crystal structure of the first bromodomain of human BRD4 in complex with SB-284847-BT Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RJ 2-(2,3-dimethylphenoxy)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidine × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB-284847-BT, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.50 Å R-free 0.180
4O7C Crystal structure of the first bromodomain of human BRD4 in complex with SB-614067-R Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RK 4-[(5Z)-5-(1-nitroso-2,3-dihydro-5H-inden-5-ylidene)-2-(piperidin-4-yl)-3,5-dihydro-4H-imidazol-4-ylidene]-1,4-dihydropyridine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB-614067-R, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.55 Å R-free 0.190
4O7E Crystal structure of the first bromodomain of human BRD4 in complex with SB-610251-B Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RN 3-[2-phenyl-4-(pyridin-4-yl)-1H-imidazol-5-yl]phenol × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB-610251-B, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.210
4O7E Crystal structure of the first bromodomain of human BRD4 in complex with SB-610251-B Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RN 3-[2-phenyl-4-(pyridin-4-yl)-1H-imidazol-5-yl]phenol × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SB-610251-B, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.85 Å R-free 0.210
4O7F Crystal structure of the first bromodomain of human BRD4 in complex with SB-251527 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RQ 4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-2-(2-methoxyphenoxy)pyrimidine × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3350, 10% DMSO, 2 MM SB-251527, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.194
4O7F Crystal structure of the first bromodomain of human BRD4 in complex with SB-251527 Deposited 2013-12-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2RQ 4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-2-(2-methoxyphenoxy)pyrimidine × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3350, 10% DMSO, 2 MM SB-251527, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.194
4OGI Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor BI-2536 Deposited 2014-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 1 R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M potassium citrate, 0.1 M Bis-Tris propane, pH 8.5, 20.0% PEG3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.73 Å R-free 0.214
4OGI Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor BI-2536 Deposited 2014-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 1 R78 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2 M potassium citrate, 0.1 M Bis-Tris propane, pH 8.5, 20.0% PEG3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.73 Å R-free 0.214
4OGJ Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor TG-101348 Deposited 2014-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 2 2TA N-tert-butyl-3-{[5-methyl-2-({4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]amino}benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20 M sodium potassium tartrate, 0.1 M Bis-Tris propane, pH 7.5, 20.0% PEG3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.65 Å R-free 0.182
4OGJ Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor TG-101348 Deposited 2014-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 1 2TA N-tert-butyl-3-{[5-methyl-2-({4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]amino}benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20 M sodium potassium tartrate, 0.1 M Bis-Tris propane, pH 7.5, 20.0% PEG3350, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.65 Å R-free 0.182
4PCE Crystal Structure of the first bromodomain of human BRD4 in complex with compound B13 Deposited 2014-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 2N0 1-benzyl-2-ethyl-1,5,6,7-tetrahydro-4H-indol-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol
Resolution 1.29 Å R-free 0.164
4PCI Crystal Structure of the first bromodomain of BRD4 in complex with B16 Deposited 2014-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2NJ (4S)-1-methyl-4-phenyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.20M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol
Resolution 1.25 Å R-free 0.169
4PS5 Crystal structure of the first bromodomain of human BRD4 in complex with TG101348 Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 2TA N-tert-butyl-3-{[5-methyl-2-({4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]amino}benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101348, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.180
4PS5 Crystal structure of the first bromodomain of human BRD4 in complex with TG101348 Deposited 2014-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 2TA N-tert-butyl-3-{[5-methyl-2-({4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]amino}benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM TG101348, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.40 Å R-free 0.180
4QB3 Crystal structure of the first bromodomain of human BRD4 in complex with Olinone Deposited 2014-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：no 30M N-[4-(1-oxo-1,2,3,4-tetrahydro-5H-pyrido[4,3-b]indol-5-yl)butyl]acetamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；293 K；25% tert-Butanol, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 0.94 Å R-free 0.155
4QR3 Brd4 Bromodomain 1 complex with its novel inhibitors Deposited 2014-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded BNJ N-cyclopentyl-3-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.37 Å R-free 0.204
4QR4 Brd4 Bromodomain 1 complex with its novel inhibitors Deposited 2014-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded BNK 2-chloro-N-cyclopentyl-5-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.28 Å R-free 0.177
4QR5 Brd4 Bromodomain 1 complex with its novel inhibitors Deposited 2014-06-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded BNM N-[3-(cyclopentylsulfamoyl)-5-(2-oxo-2,3-dihydro-1,3-thiazol-4-yl)phenyl]cyclopropanecarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol, vapor diffusion, hanging drop, temperature 293K
Resolution 1.41 Å R-free 0.194
4QZS Crystal structure of the first bromodomain of human 3-fluoro tyrosine-labeled brd4 in complex with jq1 Deposited 2014-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain residues 44-168
Non-standard monomer：Yes (specific site not provided by mmCIF) JQ1 (6S)-6-(2-tert-butoxy-2-oxoethyl)-4-(4-chlorophenyl)-2,3,9-trimethyl-6,7-dihydrothieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-10-ium × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES pH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM HEPES PH7.5, 0.1M AMMONIUM ACETATE 12.5% PEG 3,350, 10% DMSO, 1 MM JQ1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.45 Å R-free 0.185
4UIX N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-c-pyridine-2- carboxamide Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 TVU N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 293 K；0.2M CACL2, 0.1M HEPES, PEG 6K 20C
Resolution 1.58 Å R-free 0.238
4UIX N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-c-pyridine-2- carboxamide Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 TVU N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 293 K；0.2M CACL2, 0.1M HEPES, PEG 6K 20C
Resolution 1.58 Å R-free 0.238
4UIX N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-4H,5H-thieno-3,2-c-pyridine-2- carboxamide Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 TVU N-[1,1-bis(oxidanylidene)thian-4-yl]-7-(3,4-dimethoxyphenyl)-5-methyl-4-oxidanylidene-thieno[3,2-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 293 K；0.2M CACL2, 0.1M HEPES, PEG 6K 20C
Resolution 1.58 Å R-free 0.238
4UIY N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(1,1-dioxo-1-thian-4-yl)- 5-methyl-4-oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c- pyridine-2-carboximidamide Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 5V2 N-[1,1-bis(oxidanylidene)thian-4-yl]-5-methyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20% PEG3350, 0.2M KSCN, 0.1M BTP PH 7.5
Resolution 1.30 Å R-free 0.185
4UIZ N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 7-(3,4-dimethoxyphenyl)-2-(4-methanesulfonylpiperazine-1-carbonyl)-5-methyl-4H,5H-thieno-3,2-c- pyridin-4-one Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 N1D 7-(3,4-dimethoxyphenyl)-5-methyl-2-(4-methylsulfonylpiperazin-1-yl)carbonyl-thieno[3,2-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；0.1M BTP PH 6.5, 20% PEG3350, 0.2M NAFORMATE
Resolution 1.19 Å R-free 0.175
4UYD N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-dimethyl-2-oxo-2,3- dihydro-1H-1,3-benzodiazole-5-carboxamide Deposited 2014-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–183（140 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-183
Not recorded DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 V1T 1,3-dimethyl-2-oxo-2,3-dihydro-1H-benzimidazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 20% PEG3350, 0.2M NAAC
Resolution 1.37 Å R-free 0.188
4WHW Direct photocapture of bromodomains using tropolone chemical probes Deposited 2014-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 3OT 2-methoxy-4-{1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazol-5-yl}cyclohepta-2,4,6-trien-1-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Screen using Hampton Research HT and Index kits
Resolution 1.34 Å R-free 0.201
4WIV Crystal Structure of the first bromodomain of human BRD4 in complex with a novel inhibitor UMB32 (N-TERT-BUTYL-2-[4-(3,5-DIMETHYL-1,2-OXAZOL-4-YL) PHENYL]IMIDAZO[1,2-A]PYRAZIN-3-AMINE) Deposited 2014-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：unp residues 44-168
Not recorded 3P2 N-tert-butyl-2-[4-(3,5-dimethyl-1,2-oxazol-4-yl)phenyl]imidazo[1,2-a]pyrazin-3-amine × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；295 K；Crystals of inhibitor-free BRD4-BD1 were first obtained in a drop with equal volumes of BD1 at 12 mg/ml and a precipitant solution containing 100mM sodium nitrate, 5% ethylene glycol, and 18% (w/v) PEG3350, as precipitant. Rod-like crystals were typically grown in 10 days reaching a maximal size of 0.05x0.05x0.4 mm3. Then, native crystals were transferred and soaked in 1 mM UMB32 in the same crystallization buffer for 7 days.
Resolution 1.56 Å R-free 0.201
4X2I Discovery of benzotriazolo diazepines as orally-active inhibitors of BET bromodomains: Crystal structure of BRD4 with CPI-13 Deposited 2014-11-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–166（125 aa） Fragment：Bromo 1 domain (UNP residues 42-166)
Not recorded FMT FORMIC ACID × 1 3X0 (4R)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；BRD4-BD1 protein at 1mM, 2.682 M Formate, 10% Glycerol, 0.1 M Tris-HCL pH 8.5
Resolution 1.20 Å R-free 0.187
4XY9 Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand Deposited 2015-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：UNP residues 42-168
Not recorded EDO 1,2-ETHANEDIOL × 1 43U 6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M NaNO3, 20.0% PEG 3350, 10.0% EtGly
Resolution 1.83 Å R-free 0.206
4XYA Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand Deposited 2015-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：UNP residues 42-168
Not recorded 43S 6-(5-bromo-1-benzofuran-7-yl)-9H-purin-2-amine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 8.5, 0.2M sodium sulfate
Resolution 2.05 Å R-free 0.207
4YH3 Crystal structure of human BRD4(1) in complex with 4-[(2E)-3-(4-methoxyphenyl)-2-phenylprop-2-enoyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19a) Deposited 2015-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–170（127 aa） Fragment：Bromodomain 1 (UNP residues 44-170)
Not recorded Y80 4-[(2E)-3-(4-methoxyphenyl)-2-phenylprop-2-enoyl]-3,4-dihydroquinoxalin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；10% PEG3350, 0.1 M HEPES, pH 7.5, 0.2 M L-proline, soaked in 20 mM ligand for 3 hours at room temperature
Resolution 1.60 Å R-free 0.199
4YH4 Crystal structure of human BRD4(1) in complex with 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19d) Deposited 2015-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–170（127 aa） Fragment：Bromodomain 1 (UNP residues 44-170)
Not recorded Y81 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one × 1 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M potassium thiocyanate, 20% w/v PEG3350, 0.6 mM ligand
Resolution 1.33 Å R-free 0.147
4Z1Q Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine scaffold Deposited 2015-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–167（126 aa）
Not recorded 558 5-[(4R)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.5, and 25% polyethylene glycol (PEG) 3350
Resolution 1.40 Å R-free 0.242
4Z1Q Crystal structure of the first bromodomain of human BRD4 bound to benzotriazolo-diazepine scaffold Deposited 2015-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–167（126 aa）
Not recorded 558 5-[(4R)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M sodium chloride, 0.1 M Bis-Tris pH 6.5, and 25% polyethylene glycol (PEG) 3350
Resolution 1.40 Å R-free 0.242
4Z1S Crystal structure of the first bromodomain of human BRD4 with benzotriazolo-diazepine scaffold Deposited 2015-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–166（125 aa） Fragment：UNP Residues 42-166
Not recorded 559 5-[(4S)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate and 20% PEG 3350
Resolution 1.06 Å R-free 0.220
4Z1S Crystal structure of the first bromodomain of human BRD4 with benzotriazolo-diazepine scaffold Deposited 2015-03-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–166（125 aa） Fragment：UNP Residues 42-166
Not recorded 559 5-[(4S)-6-(4-chlorophenyl)-1,4-dimethyl-5,6-dihydro-4H-[1,2,4]triazolo[4,3-a][1,5]benzodiazepin-8-yl]pyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium sodium tartrate and 20% PEG 3350
Resolution 1.06 Å R-free 0.220
4Z93 BRD4 bromodomain 2 in complex with gamma-carboline-containing compound, number 18. Deposited 2015-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 349–460（112 aa） Fragment：bromodomain 2 (UNP residues 349-460)
Non-standard monomer：Yes (specific site not provided by mmCIF) 4LD 1-(3-cyclopropyl-5-methyl-1H-pyrazol-4-yl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-8-methoxy-5H-pyrido[4,3-b]indole × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；Peg 400, Imidizole, ATP
Resolution 1.27 Å R-free 0.184
4ZC9 Crystal Structure of the BRD4a/DB-2-190 complex Deposited 2015-04-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first Bromo domain (unp residues 42-167)
Not recorded 4MW 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(4-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}butyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；15% PEG3350, 0.1 M Succinate
Resolution 0.99 Å R-free 0.146
4ZW1 Crystal structure of hBRD4 in complex with BL-BI06 reveals a novel synthesized inhibitor that induces Beclin1-independent/ATG5-dependent autophagic cell death in breast cancer Deposited 2015-05-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 4V1 2-(4-hydroxy-3,5-dimethylphenyl)-7-methyl-5,6,7,8-tetrahydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4(3H)-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M ammonium phosphate dibasic, 20% PEG 3350
Resolution 1.75 Å R-free 0.249
5A5S NN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-5-methoxypyridin-3-yl-3- methyl-8-piperidin-4-ylamino-1,2-dihydro-1,7-naphthyridin-2-one Deposited 2015-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 NP8 5-(5-methoxypyridin-3-yl)-3-methyl-8-[(piperidin-4-yl)amino]-1,2-dihydro-1,7-naphthyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.2NAF, 20% PEG3350
Resolution 1.36 Å R-free 0.218
5A85 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 8-(3R,4R)-3-(cyclohexylmethoxy)piperidin-4-ylamino-3-methyl-1,2-dihydro-1,7- naphthyridin-2-one Deposited 2015-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 78J (3R,4R)-3-(cyclohexylmethoxy)piperidin-4-yl]amino}-3-methyl-1,2-dihydro-1,7-naphthyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M HEPES PH 7.0, 20% PEG 6000, 0.2M LICL
Resolution 1.72 Å R-free 0.236
5ACY N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-(2R,4S)-2-methyl-4-(phenylamino)-6-4-(piperidin-1-ylmethyl)phenyl-1,2,3,4- tetrahydroquinolin-1-yl-ethan-1-one Deposited 2015-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 3 9S3 1-[(2S,4R)-2-methyl-4-(phenylamino)-6-[4-(piperidin-1-ylmethyl)phenyl]-3,4-dihydroquinolin-1(2H)-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M MIB PH 4.0 25% PEG1500
Resolution 2.01 Å R-free 0.271
5ACY N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-(2R,4S)-2-methyl-4-(phenylamino)-6-4-(piperidin-1-ylmethyl)phenyl-1,2,3,4- tetrahydroquinolin-1-yl-ethan-1-one Deposited 2015-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded 9S3 1-[(2S,4R)-2-methyl-4-(phenylamino)-6-[4-(piperidin-1-ylmethyl)phenyl]-3,4-dihydroquinolin-1(2H)-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 0.1M MIB PH 4.0 25% PEG1500
Resolution 2.01 Å R-free 0.271
5AD2 Bivalent binding to BET bromodomains Deposited 2015-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：BROMODOMAIN 1, RESIDUES 44-168
Not recorded ETU (3R)-4-(2-{4-[1-(3-chloro[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidinyl]phenoxy}ethyl)-1,3-dimethyl-2-piperazinone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions NACL 0.2M, PEG 3350 5.9%W/V, EG 10%V/V, HEPES 0.1M PH 7.4
Resolution 2.01 Å R-free 0.236
5AD2 Bivalent binding to BET bromodomains Deposited 2015-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：BROMODOMAIN 1, RESIDUES 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions NACL 0.2M, PEG 3350 5.9%W/V, EG 10%V/V, HEPES 0.1M PH 7.4
Resolution 2.01 Å R-free 0.236
5AD3 Bivalent binding to BET bromodomains Deposited 2015-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：BROMODOMAIN 1, RESIDUES 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions PEG 4K 20%W/V, (NH4)2HPO4 0.2M
Resolution 1.49 Å R-free 0.308
5AD3 Bivalent binding to BET bromodomains Deposited 2015-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：BROMODOMAIN 1, RESIDUES 44-168
Not recorded K6K 3-methoxy-N-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)-4-piperidyl]phenoxy]ethyl]-N-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions PEG 4K 20%W/V, (NH4)2HPO4 0.2M
Resolution 1.49 Å R-free 0.308
5BT4 Crystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe Deposited 2015-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2LO 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M succinic acid, 20% PEG 3350
Resolution 1.50 Å R-free 0.214
5BT4 Crystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe Deposited 2015-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2LO 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M succinic acid, 20% PEG 3350
Resolution 1.50 Å R-free 0.214
5BT4 Crystal structure of BRD4 first bromodomain in complex with SGC-CBP30 chemical probe Deposited 2015-06-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 2LO 2-[2-(3-chloro-4-methoxyphenyl)ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(2S)-2-(morpholin-4-yl)propyl]-1H-benzimidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M succinic acid, 20% PEG 3350
Resolution 1.50 Å R-free 0.214
5CFW Selective pharmacological inhibition of the CREB binding protein bromodomain regulates inflammatory cytokines in macrophages and RGS4 in neurons Deposited 2015-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 53W 5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[2-(4-methoxyphenyl)ethyl]-1-[2-(morpholin-4-yl)ethyl]-1H-benzimidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350
Resolution 1.15 Å R-free 0.209
5COI Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded 55K 1-({[(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)sulfonyl]amino}methyl)cyclopentanecarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 7.5
Resolution 1.62 Å R-free 0.200
5CP5 Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded EB0 1-ethyl-N-(4-fluorophenyl)-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350, 0.2M (NH4)2SO4, 0.1M HEPES, 10% EtGhly, pH7.5
Resolution 1.79 Å R-free 0.242
5CPE Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 EB2 N-cycloheptyl-1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES,10% EtGhly, pH7.2
Resolution 1.62 Å R-free 0.187
5CQT Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EB3 N-cyclohexyl-1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 7.5
Resolution 1.60 Å R-free 0.191
5CRM Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-165
Not recorded NO3 NITRATE ION × 2 EB5 N,1-diethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, PH 6.5
Resolution 1.99 Å R-free 0.201
5CRZ Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 NO3 NITRATE ION × 1 EB7 2-chloro-N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)-4-fluorobenzenesulfonamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 8.0
Resolution 2.12 Å R-free 0.257
5CS8 Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP residues 44-168
Not recorded EB8 methyl 2-[(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)sulfamoyl]benzoate × 1 NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 8.3
Resolution 1.62 Å R-free 0.215
5CTL Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP residues 44-168
Not recorded EB9 N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.0
Resolution 2.51 Å R-free 0.227
5CY9 Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-07-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded GOL GLYCEROL × 1 E0A N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)butane-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；20% PEG3350, 0.2M NaCl, 0.1M HEPES, 10% EtGhly,pH 7.8
Resolution 1.55 Å R-free 0.198
5D0C Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded NO3 NITRATE ION × 3 EDO 1,2-ETHANEDIOL × 2 E0B N-[(1-acetylpiperidin-4-yl)methyl]-1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.5
Resolution 1.49 Å R-free 0.183
5D24 First bromodomain of BRD4 bound to inhibitor XD26 Deposited 2015-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：UNP residues 43-168
Mutation：T43M L26 4-acetyl-N-[3-(2-amino-2-oxoethoxy)phenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；ammonium acetate, (+/-)-2-Methyl-2,4-methylpentanediol, Bis-tris
Resolution 1.65 Å R-free 0.202
5D25 First bromodomain of BRD4 bound to inhibitor XD27 Deposited 2015-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：UNP residues 43-168
Mutation：T43M 56M 4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3,5-dimethyl-1H-pyrrole-2-carboxamide × 1 GOL GLYCEROL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Hepes
Resolution 1.70 Å R-free 0.196
5D26 First bromodomain of BRD4 bound to inhibitor XD28 Deposited 2015-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Mutation：T43M L28 N~2~-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-5-methyl-1H-pyrrole-2,4-dicarboxamide × 1 EDO 1,2-ETHANEDIOL × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Hepes, magnesium chloride
Resolution 1.82 Å R-free 0.187
5D3H First bromodomain of BRD4 bound to inhibitor XD29 Deposited 2015-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded 57G N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-4-(hydroxyacetyl)-5-methyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Bis-tris
Resolution 1.70 Å R-free 0.196
5D3J First bromodomain of BRD4 bound to inhibitor XD33 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：UNP residues 43-168
Mutation：T43M L33 4-acetyl-N-[3-(diethylsulfamoyl)phenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Hepes, magnesium chloride
Resolution 1.70 Å R-free 0.206
5D3L First bromodomain of BRD4 bound to inhibitor XD35 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：First bromodomain, UNP residues 42-168
Mutation：T43M 57F 4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxy-4-methylphenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Bis-tris, ammonium acetate
Resolution 1.50 Å R-free 0.201
5D3N First bromodomain of BRD4 bound to inhibitor XD40 Deposited 2015-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded L40 4-acetyl-3-ethyl-5-methyl-N-[2-methyl-5-(methylsulfamoyl)phenyl]-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Tacsimate
Resolution 2.15 Å R-free 0.235
5D3P First bromodomain of BRD4 bound to inhibitor XD41 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：First bromodomain, UNP residues 42-168
Mutation：T43M 57E 1-[(4-acetyl-3-ethyl-5-methyl-1H-pyrrol-2-yl)carbonyl]-N-methyl-1H-indole-6-sulfonamide × 1 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Bis-Tris, lithium sulfate
Resolution 1.95 Å R-free 0.197
5D3R First bromodomain of BRD4 bound to inhibitor XD42 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：First bromodomain, UNP residues 42-168
Mutation：T43M 57C 4-acetyl-N-[3-(azepan-1-ylsulfonyl)phenyl]-5-methyl-3-propyl-1H-pyrrole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Bis-tris, sodium chloride
Resolution 2.20 Å R-free 0.243
5D3S First bromodomain of BRD4 bound to inhibitor XD44 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Mutation：T43M 579 4-acetyl-3-ethyl-N-[4-fluoro-3-(morpholin-4-ylsulfonyl)phenyl]-5-methyl-1H-pyrrole-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, Bis-Tris
Resolution 1.75 Å R-free 0.195
5D3T First bromodomain of BRD4 bound to inhibitor XD47 Deposited 2015-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：First bromodomain, UNP residues 42-168
Mutation：T43M 56Y 4-acetyl-N-(3-carbamoylbenzyl)-3-ethyl-N,5-dimethyl-1H-pyrrole-2-carboxamide × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG3350, succinic acid
Resolution 1.93 Å R-free 0.201
5DLX FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR N-{3-[4-(3-chlorophenyl)piperazin-1-yl]propyl}-1-{3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}piperidine-4-carboxamide Deposited 2015-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5D2 N-{3-[4-(3-chlorophenyl)piperazin-1-yl]propyl}-1-(3-methyl[1,2,4]triazolo[4,3-b]pyridazin-6-yl)piperidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ratio 1:1 (protein:precipitant). 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl. Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaFormate. 1.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10 % (w/v) glycerol
Resolution 1.90 Å R-free 0.207
5DLZ FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide Deposited 2015-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5D1 N-{[1-(3-methylbenzyl)piperidin-4-yl]methyl}-4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]butanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；Ratio 1:1 (protein:precipitant) 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl.Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaNO3. 5.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10% (w/v) glycerol.
Resolution 1.70 Å R-free 0.334
5DW2 X-ray crystal structure of human BRD4(BD1) in complex with RVX297 to 1.12 A resolution Deposited 2015-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–170（127 aa） Fragment：UNP residues 44-170
Not recorded 5GD 2-{3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}-5,7-dimethoxyquinazolin-4(3H)-one × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；298 K；30% PEG2000 MME, 0.1 M potassium thiocyanate
Resolution 1.12 Å R-free 0.151
5DX4 Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand Deposited 2015-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, UNP RESIDUES 44-168
Not recorded E0C 5-bromo-N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)-2-methoxybenzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.0
Resolution 2.30 Å R-free 0.239
5E0R Crystal Structure of the first bromodomain of BRD4 in complex with AYC Deposited 2015-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5J5 2-[(chloroacetyl)amino]-5-[(E)-(4-sulfophenyl)diazenyl]benzenesulfonic acid × 5 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.20M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol
Resolution 1.35 Å R-free 0.198
5EGU FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5NQ 3-butyl-8-[(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)sulfanylmethyl]-7-ethyl-purine-2,6-dione × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol.
Resolution 2.21 Å R-free 0.235
5EGU FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5NQ 3-butyl-8-[(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)sulfanylmethyl]-7-ethyl-purine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol.
Resolution 2.21 Å R-free 0.235
5EGU FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5NQ 3-butyl-8-[(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)sulfanylmethyl]-7-ethyl-purine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol.
Resolution 2.21 Å R-free 0.235
5EGU FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 42-168
Not recorded 5NQ 3-butyl-8-[(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)sulfanylmethyl]-7-ethyl-purine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol.
Resolution 2.21 Å R-free 0.235
5EI4 First domain of human bromodomain BRD4 in complex with inhibitor 8-(5-Amino-1H-[1,2,4]triazol-3-ylsulfanylmethyl)-3-(4-chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 5NV 8-[(3-azanyl-1~{H}-1,2,4-triazol-5-yl)sulfanylmethyl]-3-[(4-chlorophenyl)methyl]-7-ethyl-purine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Ratio 1:1 (protein:precipitant). 12 mg/mL BRD4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.3M Na Formate, 0.1M NaCl, 22% PEG3350, 10% ethylene glycol. Cryoprotectant : 10% ethylene glycol.
Resolution 1.05 Å R-free 0.192
5EIS FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-(4-Chlorobenzyl)-7-ethyl-3,7-dihydropurine-2,6-dione Deposited 2015-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Mutation：NO 5OU 3-[(4-chlorophenyl)methyl]-7-ethyl-purine-2,6-dione × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；ratio 1:1 (protein:precipitant). 16 mg/mL Brd4_BD1 protein. 2.5 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.1M HEPES (pH 7.5) 0.15 mM NaCl. Precipitant agent: 19% (w/v) PEG 3350, 0.25M ammonium sulfate, 0.1M Tris pH 8.5. Cryoprotectant: 10% (w/v) ethylene glycol
Resolution 1.60 Å R-free 0.219
5F5Z Crystal structure of the first bromodomain of human BRD4 in complex with MA2-014 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 5VY 2-methyl-~{N}-[3-[[5-methyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]propane-2-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM MA2-014
Resolution 1.76 Å R-free 0.204
5F60 Crystal structure of the first bromodomain of human BRD4 in complex with SG3-014 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 5VZ ~{N}-[2-chloranyl-5-[[5-methyl-2-[[4-(4-methylpiperazin-1-yl)phenyl]amino]pyrimidin-4-yl]amino]phenyl]-2-methyl-propane-2-sulfonamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SG3-014
Resolution 1.35 Å R-free 0.171
5F61 Crystal structure of the first bromodomain of human BRD4 in complex with MA4-022-1 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 5W0 ~{N}-[3-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-5-methyl-pyrimidin-4-yl]amino]phenyl]-2-methyl-propane-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM MA4-022-1
Resolution 1.45 Å R-free 0.164
5F61 Crystal structure of the first bromodomain of human BRD4 in complex with MA4-022-1 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 7 5W0 ~{N}-[3-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-5-methyl-pyrimidin-4-yl]amino]phenyl]-2-methyl-propane-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM MA4-022-1
Resolution 1.45 Å R-free 0.164
5F62 Crystal structure of the first bromodomain of human BRD4 in complex with MA4-022-2 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 5W1 ~{N}-[2-chloranyl-5-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-5-methyl-pyrimidin-4-yl]amino]phenyl]-2-methyl-propane-2-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM MA4-022-2
Resolution 1.35 Å R-free 0.183
5F63 Crystal structure of the first bromodomain of human BRD4 in complex with SG3-179 Deposited 2015-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 5W2 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM SG3-179
Resolution 1.45 Å R-free 0.159
5FBX Crystal structure of the first bromodomain of human BRD4 in complex with PNZ5 isoxazole inhibitor Deposited 2015-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：1st bromodomain, UNP residues 44-168
Not recorded 5W4 (3~{S})-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-methyl-3-phenyl-3~{H}-isoindol-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277.15 K；20 % PEG 3350, 0.2 M zinc acetate, 0.1 M imidazole pH 7.8
Resolution 1.85 Å R-free 0.267
5H21 Trimethoxy-ring inhibitor in complex with the first bromodomain of BRD4 Deposited 2016-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：UNP RESIDUES 44-167
Not recorded RMR 3,4,5-trimethoxy-~{N}-(2-thiophen-2-ylethyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.59 Å R-free 0.190
5HCL Crystal Structure of the first bromodomain of BRD4 in complex with DMA Deposited 2016-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Not recorded 5Y9 ~{N},~{N}-dimethylethanamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.20M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol
Resolution 1.50 Å R-free 0.175
5HLS Crystal structure of the first bromodomain of human BRD4 bound to CPI-0610 Deposited 2016-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 62G CPI-0610 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；3.4-3.8 M sodium formate, 0.1 M Tris pH 7.8, and 10% glycerol
Resolution 2.18 Å R-free 0.277
5HM0 Crystal structure of the first bromodomain of human BRD4 bound to benzoisoxazoloazepine 3 Deposited 2016-01-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 62V 6-(4-chlorophenyl)-1-methyl-4H-[1,2]oxazolo[5,4-d][2]benzazepine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；3.4-3.8 M sodium formate, 0.1 M Tris pH 7.8, and 10% glycerol.
Resolution 1.40 Å R-free 0.226
5HQ5 Crystal structure of fragment bound with Brd4 Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 64Q 7-methyl-N-(o-tolyl)-[1,2,4]triazolo[4,3-a]pyrimidin-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3.6M Naformate, 10% glycerol
Resolution 1.60 Å R-free 0.187
5HQ6 Crystal structure of fragment bound with Brd4 Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded 64R (2R)-2,6-dimethyl-2H-1,4-benzoxazin-3(4H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3.6M Naformate, 10% glycerol
Resolution 1.95 Å R-free 0.204
5HQ7 Crystal structure of fragment bound with Brd4 Deposited 2016-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：UNP residues 44-167
Not recorded 64S N-ethyl-6,7-dimethoxyquinazolin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；3.6M Naformate, 10% glycerol
Resolution 1.90 Å R-free 0.211
5I80 BRD4 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide) Deposited 2016-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–167（126 aa）
Not recorded 67B N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；20% ethylene glycol, 0.1 M Bis-Tris pH 6.8, 20% polyethylene glycol (PEG) 3350
Resolution 1.45 Å R-free 0.202
5I88 BRD4 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide) Deposited 2016-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–167（126 aa）
Not recorded PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 69G 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；277 K；20% ethylene glycol, 0.1 M Bis-Tris pH 6.8, 20% polyethylene glycol (PEG) 3350
Resolution 1.40 Å R-free 0.202
5IGK Crystal structure of the first bromodomain of human BRD4 in complex with bromosporine (BSP) Deposited 2016-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 BMF Bromosporine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Na/K(tart), 0.1 M BTProp pH 8.5, 20% PEG3350, 10% EtGly
Resolution 1.70 Å R-free 0.200
5JWM Bivalent BET Bromodomain Inhibition Deposited 2016-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa） Fragment：unp residues 333-460
Not recorded 6ON 2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]-~{N}-[2-[2-[2-[2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2M ammonium sulfate, 0.1M BisTris (pH 5.5)
Resolution 1.71 Å R-free 0.168
5JWM Bivalent BET Bromodomain Inhibition Deposited 2016-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 333–460（128 aa） Fragment：unp residues 333-460
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2M ammonium sulfate, 0.1M BisTris (pH 5.5)
Resolution 1.71 Å R-free 0.168
5KDH CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH A DIHYDROPYRIDOPYRIMIDINE SCAFFOLD INHIBITOR Deposited 2016-06-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 6RX (5~{S})-1-ethyl-5-(4-methylphenyl)-8,9-dihydro-5~{H}-furo[3,4]pyrido[3,5-~{b}]pyrimidine-2,4,6-trione × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM INHIBITOR
Resolution 1.50 Å R-free 0.184
5KHM The first BET bromodomain of BRD4 bound to compound 13 in a bivalent manner Deposited 2016-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded XNH (3~{R})-4-[2-[4-[1-(3-methoxy-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)piperidin-4-yl]phenoxy]ethyl]-1,3-dimethyl-piperazin-2-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M tri-Potassium Citrate, 10% PEG 10K
Resolution 1.48 Å R-free 0.210
5KJ0 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH DB-1-264-2 Deposited 2016-06-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 6TB 4-[[(7~{R})-8-cyclopentyl-7-ethyl-5-methyl-6-oxidanylidene-7~{H}-pteridin-2-yl]-methyl-amino]-3-methoxy-~{N}-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM DB-1-264-2
Resolution 1.51 Å R-free 0.170
5KU3 BRD4 bromodomain in complex with Cpd59 ((S)-1-(3-((2-fluoro-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-1-(tetrahydrofuran-3-yl)-6,7-dihydro-1H-pyrazolo[4,3-c]pyridin-5(4H)-yl)ethanone) Deposited 2016-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–167（126 aa） Fragment：bromodomain (UNP residues 42-167)
Not recorded EDO 1,2-ETHANEDIOL × 6 DMS DIMETHYL SULFOXIDE × 2 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 6XH 1-[3-[[2-fluoranyl-4-(1-methylpyrazol-4-yl)phenyl]amino]-1-[(3~{S})-oxolan-3-yl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-5-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；287 K；0.1 M Bis-Tris pH 6.8, 18% PEG 3350, 20% ethylene glycol
Resolution 1.14 Å R-free 0.182
5LJ1 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one Deposited 2016-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 6XX 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2NaNO3, 20% PEG3350 at 20C
Resolution 1.90 Å R-free 0.237
5LJ2 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(5-aminopyridin-3-yl)-8-(((3R,4R)-3-((1,1-dioxidotetrahydro-2H-thiopyran-4-yl)methoxy)piperidin-4-yl)amino)-3-methyl-1,7-naphthyridin-2(1H)-one Deposited 2016-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 6XW 5-(5-aminopyridin-3-yl)-8-(((3R,4R)-3-((1,1-dioxidotetrahydro-2H-thiopyran-4-yl)methoxy)piperidin-4-yl)amino)-3-methyl-1,7-naphthyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 Tris pH 8.5, 0.2M Li2SO4, 20% v/v PEG400 at 20C
Resolution 1.19 Å R-free 0.208
5LRQ BRD4 in complex with ERK5 inhibitor XMD8-92 Deposited 2016-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–163（122 aa） Fragment：UNP residues 42-163
Not recorded 4WG 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；BRD4 10mg/ml 30w/v Jeffamine ED-2001 0.1M HEPES pH7.0
Resolution 1.70 Å R-free 0.233
5LUU Structure of the first bromodomain of BRD4 with a pyrazolo[4,3-c]pyridin fragment Deposited 2016-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 77X 1-(3-phenyl-1,4,6,7-tetrahydropyrazolo[4,3-c]pyridin-5-yl)propan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M Na2SO4 0.1M BTProp pH 8.5 20% PEG3350 10% EtGly
Resolution 1.61 Å R-free 0.206
5M39 Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 1 Deposited 2016-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 7EA 6-(3,4-dimethoxyphenyl)-3-methyl-[1,2,4]triazolo[4,3-b]pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；27% PEG3350 0.2M Disodium malonate 0.01 M HEPES
Resolution 1.38 Å R-free 0.242
5M39 Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 1 Deposited 2016-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa）
Not recorded 7EA 6-(3,4-dimethoxyphenyl)-3-methyl-[1,2,4]triazolo[4,3-b]pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；27% PEG3350 0.2M Disodium malonate 0.01 M HEPES
Resolution 1.38 Å R-free 0.242
5M3A Crystal structure of BRD4 BROMODOMAIN 1 IN COMPLEX WITH LIGAND 2 Deposited 2016-10-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 7E7 3-methyl-6-(1-methyl-5-phenoxy-pyrazol-4-yl)-[1,2,4]triazolo[4,3-b]pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；294 K；0.1M HEPES PEG3350 22% Di-Sodium malonate
Resolution 1.65 Å R-free 0.214
5MKZ N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 4-chloro-2-methyl-5-(((3-methylthiophen-2-yl)methyl)amino)pyridazin-3(2H)-one Deposited 2016-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded RNK 4-chloranyl-2-methyl-5-[(3-methylthiophen-2-yl)methylamino]pyridazin-3-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium nitrate 0.1 M Bis Tris propane pH 6.5 20% (w/v) PEG 3350
Resolution 1.62 Å R-free 0.169
5MLI N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 4-chloro-2-methyl-5-(methylamino)pyridazin-3(2H)-one Deposited 2016-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 82I 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M SPG buffer pH 6 25% (w/v) PEG 1500
Resolution 1.63 Å R-free 0.190
5N2M Crystal structure of the first bromodomain of human BRD4 in complex with a tetrahydroquinoline analogue Deposited 2017-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 8J2 propan-2-yl ~{N}-[(2~{S},4~{R})-6-(3-acetamidophenyl)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M NH4SO4, 25% PEG3350, 0.1M Tris pH 8.5
Resolution 1.54 Å R-free 0.230
5NNC Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.20M LiCl 0.1M TRIS pH 8.0 20.0% PEG 6K 10.0% EtGly
Resolution 2.22 Å R-free 0.265
5NNC Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；0.20M LiCl 0.1M TRIS pH 8.0 20.0% PEG 6K 10.0% EtGly
Resolution 2.22 Å R-free 0.265
5NND Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M Na(acetate) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly
Resolution 1.82 Å R-free 0.285
5NND Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M Na(acetate) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly
Resolution 1.82 Å R-free 0.285
5NNE Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated TOP2A peptide (K1201ac/K1204ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350 10% ethylene glycol 0.2M sodium iodide
Resolution 1.15 Å R-free 0.164
5NNF Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated BAZ1B peptide (K221ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 8.5 0.02M sodium/potassium phosphate
Resolution 1.15 Å R-free 0.144
5NNG Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated SRPK1 peptide (K585ac) Deposited 2017-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；30% PEG1000 0.1M PCB pH 7.0
Resolution 1.20 Å R-free 0.158
5O97 Crystal structure of human BRD4(1) bromodomain in complex with JRMBR4106 Deposited 2017-06-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 9OE (5~{Z})-4-azanyl-5-[(3-methoxy-4-oxidanyl-phenyl)methylidene]-1,3-thiazol-2-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES, pH8.0, 30% PEG5000MME
Resolution 1.30 Å R-free 0.199
5OVB Crystal structure of human BRD4(1) bromodomain in complex with DR46 Deposited 2017-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded AY2 ~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M TRIS, pH 8.5, 0.2 M Ca Acet, 25% PEG 2K MME
Resolution 1.95 Å R-free 0.193
5OVB Crystal structure of human BRD4(1) bromodomain in complex with DR46 Deposited 2017-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded AY2 ~{N}-[3-(5-ethanoyl-2-ethoxy-phenyl)-5-(1-methylpyrazol-3-yl)phenyl]furan-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M TRIS, pH 8.5, 0.2 M Ca Acet, 25% PEG 2K MME
Resolution 1.95 Å R-free 0.193
5OWM Crystal structure of human BRD4(1) bromodomain in complex with UT48 Deposited 2017-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded B0N [3-[(3-methylbenzotriazol-5-yl)methyl]phenyl]methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；HEPES, Sodium chloride
Resolution 1.50 Å R-free 0.197
5OWW Crystal structure of human BRD4(1) bromodomain in complex with UT22B Deposited 2017-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo domain 1, UNP residues 44-168
Not recorded B0Q ~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000
Resolution 1.50 Å R-free 0.203
5OWW Crystal structure of human BRD4(1) bromodomain in complex with UT22B Deposited 2017-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：Bromo domain 1, UNP residues 44-168
Not recorded B0Q ~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000
Resolution 1.50 Å R-free 0.203
5OWW Crystal structure of human BRD4(1) bromodomain in complex with UT22B Deposited 2017-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：Bromo domain 1, UNP residues 44-168
Not recorded B0Q ~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000
Resolution 1.50 Å R-free 0.203
5OWW Crystal structure of human BRD4(1) bromodomain in complex with UT22B Deposited 2017-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa） Fragment：Bromo domain 1, UNP residues 44-168
Not recorded B0Q ~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000
Resolution 1.50 Å R-free 0.203
5S9P CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YW4 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1%(w/v) Tryptone, 50mM HEPES, pH 7.0, 20%(w/v) PEG3350
Resolution 2.10 Å R-free 0.236
5S9P CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded YW4 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1%(w/v) Tryptone, 50mM HEPES, pH 7.0, 20%(w/v) PEG3350
Resolution 2.10 Å R-free 0.236
5S9P CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded YW4 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1%(w/v) Tryptone, 50mM HEPES, pH 7.0, 20%(w/v) PEG3350
Resolution 2.10 Å R-free 0.236
5S9P CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 44–168（125 aa）
Not recorded YW4 9-benzyl-2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9H-carbazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；1%(w/v) Tryptone, 50mM HEPES, pH 7.0, 20%(w/v) PEG3350
Resolution 2.10 Å R-free 0.236
5S9Q CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YW7 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；200mM Sodium Formate, pH 7.0, 20%(w/v) PEG3350
Resolution 1.85 Å R-free 0.212
5S9Q CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded YW7 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；200mM Sodium Formate, pH 7.0, 20%(w/v) PEG3350
Resolution 1.85 Å R-free 0.212
5S9Q CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded YW7 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；200mM Sodium Formate, pH 7.0, 20%(w/v) PEG3350
Resolution 1.85 Å R-free 0.212
5S9Q CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 44–168（125 aa）
Not recorded YW7 2-(3,5-dimethyl-1,2-oxazol-4-yl)-7-(2-hydroxypropan-2-yl)-9-[(S)-(oxan-4-yl)(phenyl)methyl]-9H-carbazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；200mM Sodium Formate, pH 7.0, 20%(w/v) PEG3350
Resolution 1.85 Å R-free 0.212
5S9R CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH BMS-986158, 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol Deposited 2021-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YWA 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol × 1 IOD IODIDE ION × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；100mM Bis-Tris Propane, pH 7.82, 200mM sodium iodide, 20%(w/v) PEG3350, 10% (v/v) ethylene glycol
Resolution 1.85 Å R-free 0.231
5T35 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB Deposited 2016-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 333–460（128 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；PEG 8000, Sodium citrate
Resolution 2.70 Å R-free 0.231
5T35 The PROTAC MZ1 in complex with the second bromodomain of Brd4 and pVHL:ElonginC:ElonginB Deposited 2016-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 333–460（128 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；293 K；PEG 8000, Sodium citrate
Resolution 2.70 Å R-free 0.231
5TI2 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 7635936 Deposited 2016-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Mutation：NONE 7CJ 3-fluoro-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 7635936
Resolution 1.65 Å R-free 0.181
5TI3 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 17503468 Deposited 2016-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Mutation：NONE EDO 1,2-ETHANEDIOL × 4 7CG 2,5-dibromo-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 17503468
Resolution 1.70 Å R-free 0.194
5TI4 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 8841871 Deposited 2016-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Mutation：NONE 7CM 3-chloro-4-fluoro-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 8841871
Resolution 1.62 Å R-free 0.185
5TI5 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 8841880 Deposited 2016-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Mutation：NONE 7CN 3-bromo-N-[3-(2-oxo-2,3-dihydro-1H-pyrrol-1-yl)phenyl]benzene-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 8841880
Resolution 1.83 Å R-free 0.214
5TI6 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 8841881 Deposited 2016-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Mutation：NONE 7CO 2,6-difluoro-N-[3-(2-oxopyrrolidin-1-yl)phenyl]benzene-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 8841881
Resolution 1.70 Å R-free 0.186
5TI7 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR 17528462 Deposited 2016-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 7CQ 5-bromo-2-methoxy-N-(3-(2-oxopyrrolidin-1-yl)phenyl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM 17528462
Resolution 1.65 Å R-free 0.192
5U28 BRD4 first bromodomain (BD1) in complex with dual PI3 kinase inhibitor SF2523 Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–180（137 aa）
Not recorded 82V 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one × 1 PEG DI(HYDROXYETHYL)ETHER × 1 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；40% PEG3350 (w/v) and 0.2 M potassium thiocyanate (pH 7.5)
Resolution 1.80 Å R-free 0.223
5U2C BRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 342–460（119 aa）
Not recorded 82Y N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；2.5 M ammonium sulfate in 100 mM TRIS (pH 7.5)
Resolution 3.30 Å R-free 0.296
5U2C BRD4 second bromodomain (BD2) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 342–460（119 aa）
Not recorded 82Y N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；2.5 M ammonium sulfate in 100 mM TRIS (pH 7.5)
Resolution 3.30 Å R-free 0.296
5U2E BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2535 Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–180（139 aa）
Not recorded 837 ethyl 4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；25% PEG3350 (w/v), 0.2 M ammonium chloride, 0.1 M TRIS
Resolution 1.99 Å R-free 0.240
5U2E BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2535 Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–180（139 aa）
Not recorded 837 ethyl 4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；25% PEG3350 (w/v), 0.2 M ammonium chloride, 0.1 M TRIS
Resolution 1.99 Å R-free 0.240
5U2F BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–180（139 aa）
Not recorded 82Y N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；25% PEG3350 (w/v), 0.2 M ammonium chloride, 0.1 M TRIS
Resolution 2.52 Å R-free 0.257
5U2F BRD4 first bromodomain (BD1) in complex with dual PI3 kinase (PI3K) inhibitor SF2558HA Deposited 2016-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–180（139 aa）
Not recorded 82Y N-hydroxy-4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；25% PEG3350 (w/v), 0.2 M ammonium chloride, 0.1 M TRIS
Resolution 2.52 Å R-free 0.257
5UEO BRD4_BD2_A-1395017 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 87G N-[4-(2,4-difluorophenoxy)-3-(1-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-3-yl)phenyl]ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.85 Å R-free 0.215
5UEO BRD4_BD2_A-1395017 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：residues 352-457
Not recorded 87G N-[4-(2,4-difluorophenoxy)-3-(1-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-3-yl)phenyl]ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.85 Å R-free 0.215
5UEP BRD4_BD2_A-581577 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 88P ethyl 3-methyl-4-oxo-4,5,6,7-tetrahydro-2H-isoindole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris 7.0
Resolution 1.77 Å R-free 0.219
5UEQ BRD4_BD2_A-1390146 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 87M N-[3-(7-methyl-1-oxo-2,6-dihydro-1H-pyrrolo[3,4-d]pyridazin-5-yl)-4-phenoxyphenyl]ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.70 Å R-free 0.217
5UER BRD4_BD2_A-1359930 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 87P N-[3-(3-methyl-4-oxo-4,5,6,7-tetrahydro-2H-isoindol-1-yl)-4-phenoxyphenyl]methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.87 Å R-free 0.243
5UES BRD4_BD2_A-1344772 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 87S 5-[2-(4-chlorophenoxy)phenyl]-2-methyl-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.62 Å R-free 0.225
5UET BRD4_BD2_A-1308586 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 87V 2-methyl-5-phenyl-1H-pyrrole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.29 Å R-free 0.254
5UEU BRD4_BD2_A-1107604 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 0S6 methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.26 Å R-free 0.221
5UEU BRD4_BD2_A-1107604 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：residues 352-457
Not recorded 0S6 methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.26 Å R-free 0.221
5UEV BRD4_BD2_A-556343 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 88Y 1-[5-(2-aminophenyl)-2-methyl-1H-pyrrol-3-yl]ethan-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.94 Å R-free 0.237
5UEX BRD4_BD2_A-1497627 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 89D 17-{[ethyl(dihydroxy)-lambda~4~-sulfanyl]amino}-11,13-difluoro-2-methyl-6,7,8,9-tetrahydrodibenzo[4,5:7,8][1,6]dioxacyclododecino[3,2-c]pyridin-3(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100mM NaCl, 5 mM DTT Crystallization : 15 % (v/v) Ethanol, Tris PH 7.0
Resolution 2.29 Å R-free 0.279
5UEY BRD4_BD2_A-1412838 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 88M 5-[2-(2,4-difluorophenoxy)-5-{[ethyl(dihydroxy)-lambda~4~-sulfanyl]amino}phenyl]-4-ethoxy-1-methylpyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.41 Å R-free 0.310
5UEZ BRD4_BD2_A-1342843 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 89G 5-methoxy-2-methyl-6-(2-phenoxyphenyl)pyridazin-3(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 %(v/v) Ethanol Tris PH 7.0
Resolution 1.51 Å R-free 0.204
5UF0 BRD4_BD2-A-35165 Deposited 2017-01-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 89J 2-methyl-5-(methylamino)-6-phenylpyridazin-3(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；Protein buffer : PH 7.5 10 mM HEPES 100 mM NaCl 5mM DTT Crystallization : 15 %(V/V) Ethanol Tris PH 7.0
Resolution 1.35 Å R-free 0.201
5ULA Crystal Structure of the First Bromodomain of Human BRD4 in Complex With Cyclic Vinylogous Amide Inhibitor MS402 Deposited 2017-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5MJ 3-chloranyl-~{N}-(4-methoxyphenyl)-4-[(2-methyl-3-oxidanylidene-cyclopenten-1-yl)amino]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4.3 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Resolution 1.50 Å R-free 0.178
5ULA Crystal Structure of the First Bromodomain of Human BRD4 in Complex With Cyclic Vinylogous Amide Inhibitor MS402 Deposited 2017-01-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded 5MJ 3-chloranyl-~{N}-(4-methoxyphenyl)-4-[(2-methyl-3-oxidanylidene-cyclopenten-1-yl)amino]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4.3 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Resolution 1.50 Å R-free 0.178
5UOO BRD4 bromodomain 2 in complex with CD161 Deposited 2017-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa） Fragment：UNP residues 333-460
Non-standard monomer：Yes (specific site not provided by mmCIF) 8FV 7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；60% peg 400, 0.1M Imidizole, 5mM ATP
Resolution 1.69 Å R-free 0.196
5UVS BRD4_BD2_A-1406537 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8O1 4-{2-[(cyclopropylmethyl)amino]-5-(ethylsulfonyl)phenyl}-6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.15 Å R-free 0.247
5UVT BRD4_BD2_A-1454056 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NV 7-(cyclopropylmethyl)-2-methyl-10-[(propan-2-yl)sulfonyl]-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.67 Å R-free 0.193
5UVU BRD4_BD2_A-1461028 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8O4 7-(cyclopropylmethyl)-2-methyl-10-[(methylsulfonyl)methyl]-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 MM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol, Tris PH 7.0
Resolution 1.66 Å R-free 0.212
5UVV BRD4 Bromodomain 2 with A-1457066 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NS 7-(cyclopropylmethyl)-10-(ethylsulfonyl)-2-methyl-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.99 Å R-free 0.301
5UVV BRD4 Bromodomain 2 with A-1457066 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NS 7-(cyclopropylmethyl)-10-(ethylsulfonyl)-2-methyl-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.99 Å R-free 0.301
5UVW BRD4_Bromodomain1-A1376855 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 57–165（109 aa） Fragment：residues 57-165
Not recorded 8NG N-[4-(2,4-difluorophenoxy)-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)phenyl]ethanesulfonamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.14 Å R-free 0.226
5UVW BRD4_Bromodomain1-A1376855 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–165（109 aa） Fragment：residues 57-165
Not recorded 8NG N-[4-(2,4-difluorophenoxy)-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)phenyl]ethanesulfonamide × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.14 Å R-free 0.226
5UVW BRD4_Bromodomain1-A1376855 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 57–165（109 aa） Fragment：residues 57-165
Not recorded 8NG N-[4-(2,4-difluorophenoxy)-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)phenyl]ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.14 Å R-free 0.226
5UVX BRD4 Bromodomain 2 with A-1359643 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NM N-[3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-4-phenoxyphenyl]methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.53 Å R-free 0.197
5UVX BRD4 Bromodomain 2 with A-1359643 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NM N-[3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-4-phenoxyphenyl]methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.53 Å R-free 0.197
5UVY BRD4 Bromodomain 2 with A-1349391 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NJ 6-methyl-4-(2-phenoxyphenyl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.25 Å R-free 0.262
5UVY BRD4 Bromodomain 2 with A-1349391 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NJ 6-methyl-4-(2-phenoxyphenyl)-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 2.25 Å R-free 0.262
5UVZ BRD4 Bromodomain 2 with A-1354689 Deposited 2017-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：residues 352-457
Not recorded 8NP 3-methyl-5-(2-phenoxyphenyl)pyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris PH 7.0
Resolution 1.63 Å R-free 0.225
5V67 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH Volasertib Deposited 2017-03-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded IBI N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide × 1 EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM Volasertib
Resolution 1.78 Å R-free 0.208
5VBO CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH LRRK2-IN-1 Deposited 2017-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded 4K4 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 55MM HEPES PH 7.5, 15% Jeffamine ED-2001 pH 7.0, 10% DMSO, 1 MM LRRK2-IN-1
Resolution 1.30 Å R-free 0.164
5VBP CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH RO3280 Deposited 2017-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 79C 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM RO3280
Resolution 1.83 Å R-free 0.207
5VBP CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH RO3280 Deposited 2017-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP RESIDUES 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 79C 4-[(9-cyclopentyl-7,7-difluoro-5-methyl-6-oxo-6,7,8,9-tetrahydro-5H-pyrimido[4,5-b][1,4]diazepin-2-yl)amino]-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM RO3280
Resolution 1.83 Å R-free 0.207
5VOM Benzopiperazine BET bromodomain inhibitor in complex with BD1 of Brd4 Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 9GY 3-[(2S)-1-acetyl-4-(furan-2-carbonyl)-2-methyl-1,2,3,4-tetrahydroquinoxalin-6-yl]-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；30% PEG 4000, 0.1 M MES pH 6.8
Resolution 1.67 Å R-free 0.218
5VOM Benzopiperazine BET bromodomain inhibitor in complex with BD1 of Brd4 Deposited 2017-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded 9GY 3-[(2S)-1-acetyl-4-(furan-2-carbonyl)-2-methyl-1,2,3,4-tetrahydroquinoxalin-6-yl]-N-methylbenzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；30% PEG 4000, 0.1 M MES pH 6.8
Resolution 1.67 Å R-free 0.218
5VZS BRD4-BD1 in complex with Cpd19 (3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-N-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide) Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BRD4 Bromodomain-1, UNP residues 42-168
Not recorded EDO 1,2-ETHANEDIOL × 1 9U4 3-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-N-methyl-1-(oxan-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；20% PEG 3350, 0.2 M sodium formate
Resolution 1.71 Å R-free 0.226
5VZS BRD4-BD1 in complex with Cpd19 (3-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-N-methyl-1-(tetrahydro-2H-pyran-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide) Deposited 2017-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa） Fragment：BRD4 Bromodomain-1, UNP residues 42-168
Not recorded EDO 1,2-ETHANEDIOL × 2 9U4 3-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-N-methyl-1-(oxan-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；20% PEG 3350, 0.2 M sodium formate
Resolution 1.71 Å R-free 0.226
5W55 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG048 Deposited 2017-06-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：residues 42-168
Not recorded X30 11-ethyl-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.35 Å R-free 0.195
5WA5 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor XMD11-50 Deposited 2017-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：Bromodomain residues 42-168
Not recorded 4K4 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.17 Å R-free 0.158
5WMA N-terminal bromodomain of BRD4 in complex with PLX5981 Deposited 2017-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-terminal bromodomain (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 1 6JC 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-pyrrolo[2,3-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Bis-Tris propane, pH 7.5-8.0, 11% PEG3350, 0.2 M sodium chloride, 20% ethylene glycol
Resolution 1.40 Å R-free 0.176
5WMD N-terminal bromodomain of BRD4 in complex with OTX-015 Deposited 2017-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-terminal bromodomain (UNP residues 44-168)
Mutation：D96A 6JE 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(4-hydroxyphenyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Bis-Tris, pH 7.5, 19% PEG3350, 0.2 M lithium sulfate
Resolution 1.27 Å R-free 0.170
5WMG N-terminal bromodomain of BRD4 in complex with OTX-015 Deposited 2017-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：N-terminal bromodomain (UNP residues 44-168)
Mutation：D96A EDO 1,2-ETHANEDIOL × 3 6JF 4-{6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1S)-1-(pyridin-2-yl)ethyl]-1H-pyrrolo[3,2-b]pyridin-3-yl}benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M Bis-Tris, pH 7.5, 19% PEG3350, 0.2 M lithium sulfate
Resolution 1.19 Å R-free 0.146
5WUU Complex structure of the first bromodomain of BRD4 with an inhibitor that containing a 2H-chromen-2-one ring Deposited 2016-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：UNP RESIDUES 44-167
Not recorded 7UU ~{N}-methyl-~{N}-[3-[(2-oxidanylidenechromen-4-yl)amino]propyl]thiophene-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.72 Å R-free 0.205
5XHY BRD4 bound with compound Bdi1 Deposited 2017-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded 8FC ~{N}-(4-cyclopropyl-1,3,3-trimethyl-2-oxidanylidene-quinoxalin-6-yl)-4-methyl-benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, PH 6.5
Resolution 1.98 Å R-free 0.285
5XI2 BRD4 bound with compound Bdi2 Deposited 2017-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded 8F9 (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{S})-1-(4-methylphenyl)ethyl]amino]-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.5M NAFORMATE, 5% GLYCEROL
Resolution 1.91 Å R-free 0.237
5XI3 BRD4 bound with compound Bdi3 Deposited 2017-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded 8F6 (3~{R})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{R})-1-phenylethyl]amino]-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.5M NAFORMATE, 5% GLYCEROL
Resolution 1.67 Å R-free 0.218
5XI4 BRD4 bound with compound Bdi4 Deposited 2017-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded 8F0 (3~{S})-4-cyclopropyl-1,3-dimethyl-6-[[(1~{S})-1-(4-methylphenyl)ethyl]amino]-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.3 M NAFORMATE, 10% GLYCEROL
Resolution 1.49 Å R-free 0.253
5Y1Y Complex structure of nitroxoline with the first bromodomain of BRD4 Deposited 2017-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：UNP residues 44-167
Not recorded HNQ 5-nitroquinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.91 Å R-free 0.224
5Y8C Crystal Structure Analysis of the BRD4 Deposited 2017-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：UNP residues 44-166
Not recorded NO3 NITRATE ION × 2 8P9 5-chloranyl-2-methoxy-N-(6-methoxy-3-methyl-1,2-benzoxazol-5-yl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 8.2
Resolution 1.42 Å R-free 0.214
5Y8W Crystal Structure Analysis of the BRD4 Deposited 2017-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 8PU 5-bromanyl-2-methoxy-N-(3-methyl-6-oxidanyl-1,2-benzoxazol-5-yl)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 5 NO3 NITRATE ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH8.2
Resolution 1.76 Å R-free 0.236
5Y8Y Crystal Structure Analysis of the BRD4 Deposited 2017-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded NO3 NITRATE ION × 3 EDO 1,2-ETHANEDIOL × 2 8PX 5-bromanyl-2-methoxy-N-(6-methoxy-3-methyl-1,2-benzoxazol-5-yl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH7
Resolution 1.87 Å R-free 0.247
5Y8Z Crystal Structure Analysis of the BRD4 Deposited 2017-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 8Q3 5-bromanyl-N-(3,6-dimethyl-1,2-benzoxazol-5-yl)-2-methoxy-benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 NO3 NITRATE ION × 2 NA SODIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH7.2
Resolution 1.84 Å R-free 0.184
5Y93 Crystal Structure Analysis of the BRD4 Deposited 2017-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 8Q9 2-[[5-[(5-bromanyl-2-methoxy-phenyl)sulfonylamino]-3-methyl-1,2-benzoxazol-6-yl]oxy]-N-(2-morpholin-4-ylethyl)ethanamide × 1 NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH8.3
Resolution 1.62 Å R-free 0.210
5Y94 Crystal Structure Analysis of the BRD4 Deposited 2017-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 8QC 5-bromanyl-2-methoxy-N-[3-methyl-6-(methylamino)-1,2-benzoxazol-5-yl]benzenesulfonamide × 1 NO3 NITRATE ION × 2 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH8.0
Resolution 2.00 Å R-free 0.223
5YOU Crystal structure of BRD4-BD1 bound with hjp64 Deposited 2017-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Mutation：T43M 8XX (3~{R})-4-cyclopropyl-~{N},1,3-trimethyl-~{N}-(4-methylphenyl)-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol
Resolution 1.50 Å R-free 0.248
5YOV Crystal structure of BRD4-BD1 bound with hjp126 Deposited 2017-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Mutation：T43M 8XR (3~{R})-4-cyclopentyl-~{N}-(2,4-dimethylphenyl)-1,3-dimethyl-2-oxidanylidene-3~{H}-quinoxaline-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.6M Naformate, 10% glycerol
Resolution 1.45 Å R-free 0.231
5YQX Crystal Structure Analysis of the BRD4 Deposited 2017-11-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded E0K (2R)-2-(cyclopropylmethyl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-4H-1,4-benzoxazin-3-one × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES pH 7.5, 20% PEG 3350, 10% EtGhly, 0.2M NaCl
Resolution 1.82 Å R-free 0.219
5Z1R Crystal Structure Analysis of the BRD4 Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain
Not recorded EFL 5-bromo-N-(2,2-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-2-methoxybenzene-1-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.1M HEPES, 10% EtGhly, PH8.2
Resolution 1.62 Å R-free 0.193
5Z1S Crystal Structure Analysis of the BRD4(1) Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain
Not recorded EFM 5-bromo-2-methoxy-N-(6-methoxy-2,2-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)benzene-1-sulfonamide × 1 NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.1M HEPES, 10% EtGhly, PH7.0
Resolution 1.42 Å R-free 0.220
5Z1T Crystal Structure Analysis of the BRD4(1) Deposited 2017-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain
Not recorded EFN 5-bromo-N-(6-hydroxy-2,2-dimethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-2-methoxybenzene-1-sulfonamide × 1 NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.1M HEPES, 10% EtGhly, PH7.5
Resolution 1.42 Å R-free 0.211
5Z5T The first bromodomain of BRD4 with compound BDF-2141 Deposited 2018-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：first bromodomain
Not recorded 96R 2-amino-4-(1H-imidazol-1-yl)quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.99 Å R-free 0.243
5Z5U The first bromodomain of BRD4 with compound BDF-2254 Deposited 2018-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：first bromodomain
Not recorded 96U 2-amino-4-(1H-imidazol-1-yl)quinoline-6,8-diol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.63 Å R-free 0.215
5Z5V The first bromodomain of BRD4 with compound BDF-1253 Deposited 2018-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa） Fragment：BD1 domain
Not recorded 96X N-{8-hydroxy-4-[(1H-imidazol-1-yl)methyl]quinolin-2-yl}acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.66 Å R-free 0.219
5Z8G BRD4 Bromodomain 1 with an inhibitor Deposited 2018-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromodomain 1
Not recorded 99L 1-ethyl-6-[(3R)-3-oxidanylpiperidin-1-yl]sulfonyl-benzo[cd]indol-2-one × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；4M sodium formate, 15% glycerol
Resolution 1.70 Å R-free 0.211
5Z8R BRD4 Bromodomain 1 with an inhibitor Deposited 2018-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromodomain 1
Not recorded 99O 1-ethyl-6-[(3S)-3-oxidanylpiperidin-1-yl]sulfonyl-benzo[cd]indol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate, 15% glycerol
Resolution 2.00 Å R-free 0.253
5Z8Z BRD4 Bromodomain 1 with an inhibitor Deposited 2018-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromodomain 1
Not recorded 99R 6-[(3S)-3-azanylpiperidin-1-yl]sulfonyl-1-ethyl-benzo[cd]indol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate, 15% glycerol
Resolution 1.80 Å R-free 0.238
5Z90 BRD4 Bromodomain 1 with an inhibitor Deposited 2018-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromodomain 1
Not recorded 99U 1-ethyl-6-pyrrolidin-1-ylsulfonyl-benzo[cd]indol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate, 15% glycerol
Resolution 1.80 Å R-free 0.264
5Z9C Solution NMR structures of BRD4 first bromodomain with small compound MMQO Deposited 2018-02-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 53–168（116 aa）
Not recorded MQO 8-methoxy-6-methylquinolin-4(1H)-one × 1 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) null；Pressure 1
NMR sample composition 100 mM NACL, 10 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5Z9K BRD4 Bromodomain 1 with an inhibitor Deposited 2018-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromodomain 1
Not recorded 99X 1-ethyl-6-[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]sulfonyl-benzo[cd]indol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate, 15% glycerol
Resolution 1.89 Å R-free 0.258
6AFR Crystal Structure of the first bromodomain of human BRD4 in complex with 5-((4-fluoro-1H-imidazol-1-yl)methyl)quinolin-8-ol Deposited 2018-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded 9E3 5-[(4-fluoranylimidazol-1-yl)methyl]quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；289.15 K；The protein was concentrated to 8-10 mg mL-1 in the buffer containing 20mM HEPES, pH7.4, 100mM NaCl and 1mM DTT. The apo crystals of BRD4_BD1 were harvested by using sitting drop vapor-diffusion method in 4M sodium formate and 15% glycerol at 289.15K. Then the apo crystals were soaked into reservoir solution containing 1mM compound for 7 days.
Resolution 2.00 Å R-free 0.268
6AJV Crystal structure of BRD4 in complex with isoliquiritigenin and DMSO (Cocktail No. 3) Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded NA SODIUM ION × 3 HCC 2',4,4'-TRIHYDROXYCHALCONE × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；4M sodium formate, 0.1M tris-HCl pH 8.0
Resolution 1.45 Å R-free 0.227
6AJW Crystal structure of BRD4 in complex with DMSO (Cocktail No. 4) Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded NA SODIUM ION × 3 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；4M sodium formate, 0.1M tris-HCl pH 8
Resolution 1.40 Å R-free 0.228
6AJX Crystal structure of BRD4 in complex with isoliquiritigenin in the absence of DMSO Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded HCC 2',4,4'-TRIHYDROXYCHALCONE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4M sodium formate, 0.1M tris-HCl pH 8
Resolution 1.89 Å R-free 0.237
6AJY Crystal structure of BRD4 in complex with 2',4'-dihydroxy-2-methoxychalcone Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded A0R 2',4'-dihydroxy-2-methoxychalcone × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；4M sodium formate, 0.1M tris-HCl pH 8
Resolution 1.60 Å R-free 0.220
6AJZ Joint nentron and X-ray structure of BRD4 in complex with colchicin Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded LOC N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 NA SODIUM ION × 1 Experimental method not declared
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.9M sodium formate, 17mM Tris, 83mM Tris-HCl in D2O
Resolution not provided
6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 42–168（127 aa）
Mutation：T43M ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 42–168（127 aa）
Mutation：T43M, D145A ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.99 Å R-free 0.333
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 42–168（127 aa） Fragment：residues 42-168
Mutation：T43M Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
Resolution 6.34 Å R-free 0.381
6BNH Solution NMR structures of BRD4 ET domain with JMJD6 peptide Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 601–683（83 aa） Fragment：ET domain residues 601-683
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure 1
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
Resolution not provided
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 42–168（127 aa） Fragment：residues 42-168
Mutation：T43M ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 3.33 Å R-free 0.234
6C7Q BRD4 BD2 in complex with compound CE277 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EO1 7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-N-(1-methyl-1H-indazol-3-yl)-9H-pyrimido[4,5-b]indol-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；50-75% peg 400, 0.1M Imidizole, pH 8.0
Resolution 1.51 Å R-free 0.225
6C7R BRD4 BD1 in complex with compound CF53 Deposited 2018-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–165（122 aa）
Not recorded EO4 N-(3-cyclopropyl-1-methyl-1H-pyrazol-5-yl)-7-(3,5-dimethyl-1,2-oxazol-4-yl)-6-methoxy-2-methyl-9H-pyrimido[4,5-b]indol-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% peg 3350, 0.2M Potassium Chloride
Resolution 1.50 Å R-free 0.241
6CD4 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG046 Deposited 2018-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：residues 44-168
Not recorded EX1 2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-11-(propan-2-yl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.23 Å R-free 0.168
6CD5 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor XMD17-26 Deposited 2018-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：residues 44-168
Not recorded R4L 11-cyclopentyl-2-[[2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl-phenyl]amino]-5-methyl-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 3 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.58 Å R-free 0.193
6CIS Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG047 Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：residues 44-166
Not recorded X26 11-cyclopentyl-5-methyl-2-({4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]-2-[(propan-2-yl)oxy]phenyl}amino)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 3 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.51 Å R-free 0.216
6CIY Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG069 Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：residues 44-168
Not recorded F3J 11-cyclobutyl-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 2 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.68 Å R-free 0.207
6CJ1 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG071 Deposited 2018-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：residues 44-166
Not recorded F2S 11-[(2R)-butan-2-yl]-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 FND 11-[(2S)-butan-2-yl]-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 3 NO3 NITRATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.53 Å R-free 0.192
6CJ2 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG056 Deposited 2018-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–166（125 aa） Fragment：residues 42-166
Not recorded X27 2-{[3-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5-methyl-11-(propan-2-yl)-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；100mM Sodium Nitrate, 5% Ethylene Glycol, 18% (w/v) PEG3350
Resolution 1.47 Å R-free 0.214
6CKR Crystal Structure of BRD4 with QC4956 Deposited 2018-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded F5V N-{3-[2-methyl-6-(1-methyl-1H-pyrazol-4-yl)-1-oxo-1,2-dihydroisoquinolin-4-yl]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG3350, 50 mM HEPES, pH 7.5
Resolution 1.62 Å R-free 0.238
6CKR Crystal Structure of BRD4 with QC4956 Deposited 2018-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded F5V N-{3-[2-methyl-6-(1-methyl-1H-pyrazol-4-yl)-1-oxo-1,2-dihydroisoquinolin-4-yl]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；15% PEG3350, 50 mM HEPES, pH 7.5
Resolution 1.62 Å R-free 0.238
6CKS Crystal Structure of BRD4 with QC4956 Deposited 2018-02-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded F5Y 4-[5-(ethylsulfonyl)-2-methoxyphenyl]-2-methyl-6-(1-methyl-1H-pyrazol-4-yl)isoquinolin-1(2H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG6000, 50 mM TRIS, pH 7.7, 5% ethylene glycol
Resolution 1.72 Å R-free 0.211
6CZU BRD4(BD1) complexed with 3219 Deposited 2018-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–170（129 aa）
Not recorded FP7 5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-({4-[(1R)-1-hydroxyethyl]phenyl}methyl)pyridin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 7 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；0.2 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350
Resolution 1.47 Å R-free 0.194
6CZV BRD4(BD1) complexed with 2759 Deposited 2018-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–170（129 aa）
Not recorded FOY 1-benzyl-5-(3,5-dimethyl-1,2-oxazol-4-yl)pyridin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2 M Potassium Fluoride, 8% (w/v) PEG 3,350
Resolution 1.88 Å R-free 0.226
6DJC Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS645 Deposited 2018-05-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–173（130 aa）
Chain B 44–173（130 aa）
Not recorded CF6 N,N'-(decane-1,10-diyl)bis{2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide} × 1 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium sulfate, 0.1M Bis-Tris pH6.5, 25% w/v Polyethylene glycol 3350
Resolution 1.46 Å R-free 0.176
6DL2 BRD4 bromodomain 1 in complex with HYB157 Deposited 2018-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded GUJ 3-benzyl-2,9-dimethyl-4H,6H-thieno[2,3-e][1,2,4]triazolo[3,4-c][1,4]oxazepine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16% Peg 3350, 0.2 M Potassium Chloride
Resolution 1.47 Å R-free 0.216
6DMJ A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain Deposited 2018-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 53W 5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-[2-(4-methoxyphenyl)ethyl]-1-[2-(morpholin-4-yl)ethyl]-1H-benzimidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 3350
Resolution 1.15 Å R-free 0.194
6DML A multiconformer ligand model of 3,5 dimethylisoxaxole bound to the bromodomain of human BRD4 Deposited 2018-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 9BM 4-((2-(tert-butyl)phenyl)amino)-7-(3,5-dimethylisoxazol-4-yl)-6-methoxy-1,5-naphthyridine-3-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350, 0.2M NANO3, 0.1M BIS-TRIS-PROPANE PH8.5
Resolution 1.50 Å R-free 0.192
6DNE Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS660 Deposited 2018-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–477（434 aa）
Not recorded H1V N,N'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis{2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide} × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG 4000 0.1M TrisHCl pH8.5 0.2M Mg Chloride
Resolution 2.96 Å R-free 0.285
6DNE Crystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS660 Deposited 2018-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–477（434 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；30% PEG 4000 0.1M TrisHCl pH8.5 0.2M Mg Chloride
Resolution 2.96 Å R-free 0.285
6DUV Crystal structure of the second bromodomain of human BRD4 in complex with MS417 inhibitor Deposited 2018-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 347–458（112 aa） Fragment：BRD4 second bromodomain
Not recorded 0S6 methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 10.5；290 K；2.0 Ammonium Sulfate, 0.2 M Lithium Sulfate, CAPS pH10.5
Resolution 1.80 Å R-free 0.188
6DUV Crystal structure of the second bromodomain of human BRD4 in complex with MS417 inhibitor Deposited 2018-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 347–458（112 aa） Fragment：BRD4 second bromodomain
Not recorded 0S6 methyl [(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 10.5；290 K；2.0 Ammonium Sulfate, 0.2 M Lithium Sulfate, CAPS pH10.5
Resolution 1.80 Å R-free 0.188
6E4A Crystal structure of human BRD4(1) in complex with CN750 Deposited 2018-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–170（127 aa）
Not recorded HRY 5-(4-{[(3-chlorophenyl)methyl]amino}-2-{4-[2-(dimethylamino)ethyl]piperazin-1-yl}quinazolin-6-yl)-1-methylpyridin-2(1H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；100 mM TrisHCl pH 8.5, 25% PEG 3350
Resolution 1.26 Å R-free 0.189
6E4A Crystal structure of human BRD4(1) in complex with CN750 Deposited 2018-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–170（127 aa）
Not recorded HRY 5-(4-{[(3-chlorophenyl)methyl]amino}-2-{4-[2-(dimethylamino)ethyl]piperazin-1-yl}quinazolin-6-yl)-1-methylpyridin-2(1H)-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；100 mM TrisHCl pH 8.5, 25% PEG 3350
Resolution 1.26 Å R-free 0.189
6FFD Human BRD4 C-terminal bromodomain with 1-(4-(3-methylbenzyl)-3,4-dihydroquinoxalin-1(2H)-yl)ethanone Deposited 2018-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 347–463（117 aa） Fragment：UNP residues 347-463
Not recorded D7T 1-(4-(3-methylbenzyl)-3,4-dihydroquinoxalin-1(2H)-yl)ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M morpheus buffer1, pH 6.5, 30% morpheus EDO_P8K, 0.12M Morpheus alchol mixture
Resolution 1.83 Å R-free 0.253
6FNX FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR F1 Deposited 2018-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded DYZ 7-ethyl-3-(phenylmethyl)purine-2,6-dione × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；292 K；5mM of #F1 inhibitor (in DMSO) final concentration. Ratio 1:1 (protein:precipitant). 20mg/mL of BRD4(BD1) protein. 0.25M AmSO4; 0.1M NaCl; 0,1M Tris pH 8.5; 19% (w/v) PEG3350. Cryoprotectant: 10 % (w/v) ethylene glycol.
Resolution 1.19 Å R-free 0.276
6FO5 FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR #17 Deposited 2018-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded DZH ~{N}-[[4-[[7-ethyl-2,6-bis(oxidanylidene)purin-3-yl]methyl]phenyl]methyl]-2-oxidanylidene-1,3,4,5-tetrahydro-1-benzazepine-7-sulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；292 K；2.5mM of #17 inhibitor (in DMSO) final concentration. Ratio 1:1 (protein:precipitant. 12mg/mL of BRD4(BD1) protein. Precipitant agent: 0.3M NaNO3; 0.1M NaCl; 22% (w/v) PEG3350; 10% (w/v) ethylene glycol. Cryoprotectant: 10 % (w/v) glycerol.
Resolution 0.95 Å R-free 0.154
6FSY Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2018-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 E5Q 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(~{R})-oxidanyl(pyridin-3-yl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20 % PEG 3350 and 0.1 M citrate pH 5.5
Resolution 1.34 Å R-free 0.200
6FT3 Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2018-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 E5T 3-[(~{R})-cyclopropyl(oxidanyl)methyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M K(citrate) 0.1 M cacodylate pH 6.5
Resolution 1.28 Å R-free 0.184
6FT4 Crystal Structure of the first bromodomain of human BRD4 in complex with a 3,5-dimethylisoxazol ligand Deposited 2018-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded E5W 3-[[4,4-bis(fluoranyl)piperidin-1-yl]methyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；30% PEG1000 0.1M MMT pH 6.0
Resolution 1.34 Å R-free 0.217
6G0D BRD4 (BD1) in complex with APSC-derived ligands (e.g. LY294002) Deposited 2018-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BD1
Mutation：T43M EDO 1,2-ETHANEDIOL × 1 LY2 2-MORPHOLIN-4-YL-7-PHENYL-4H-CHROMEN-4-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.2 M sodium fluoride, 20 % (w/v) PEG 3350, cryo protection: 20% ethylene glycol
Resolution 1.31 Å R-free 0.236
6G0E BRD4 (BD1) in complex with APSC-derived ligands Deposited 2018-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BD1
Mutation：T43M EGN 4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one × 1 FMT FORMIC ACID × 2 NA SODIUM ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；0.1 M sodium acetate pH 4.6, 3.5 M sodium formate, cryo protection: 20% glycero
Resolution 1.61 Å R-free 0.261
6G0F BRD4 (BD1) in complex with docking-derived ligand Deposited 2018-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BD1
Mutation：T43M EDO 1,2-ETHANEDIOL × 1 EGH (4~{R})-4-(5-bromanyl-2-fluoranyl-phenyl)-5,6,7-trimethoxy-3,4-dihydro-1~{H}-quinolin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M Tri-sodium citrate pH 6.5, cryo protection: 20% ethylene glycol
Resolution 1.62 Å R-free 0.229
6G0G BRD4 (BD1) in complex with APSC-derived ligands (e.g. sulfasalazine) Deposited 2018-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BD1
Mutation：T43M EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 DMS DIMETHYL SULFOXIDE × 1 SAS 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1 M sodium acetate anhydrous pH 4.6 and 3.5 M sodium formate, cryo protection: 25% ethylene glycol
Resolution 1.48 Å R-free 0.220
6G0H BRD4 (BD1) in complex with APSC-derived ligands (e.g. SSLH01 a sulfasalazine derivate) Deposited 2018-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa） Fragment：BD1
Mutation：T43M EDO 1,2-ETHANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 EGE 4-azanyl-2-oxidanyl-5-[(~{E})-[4-(pyridin-2-ylsulfamoyl)phenyl]diazenyl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；0.1 M sodium acetate anhydrous pH 4.6 and 3.5 M sodium formate, cryo protection: 25% ethylene glycol
Resolution 1.91 Å R-free 0.226
6G0O Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated ATRX peptide (K1030ac/K1033ac) Deposited 2018-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.2 M LiCl
Resolution 1.40 Å R-free 0.166
6G0P Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated E2F1 peptide (K117ac/K120ac) Deposited 2018-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG3350 10.0 % EtGly 0.2 M NaCHO
Resolution 1.30 Å R-free 0.147
6G0Q Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated GATA1 peptide (K312ac/K315ac) Deposited 2018-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；30.0% PEG 1k 0.1M SPG pH 8.0
Resolution 1.40 Å R-free 0.178
6G0R Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated POLR2A peptide (K775ac/K778ac) Deposited 2018-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.1 M MgCl2
Resolution 1.25 Å R-free 0.175
6G0S Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated SIRT7 peptide (K272ac/K275ac) Deposited 2018-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa）
Chain B 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20.0 % PEG3350 10.0 % EtGly 0.1 M bis-tris-propane pH 8.5 0.2M NaOOCCH3
Resolution 1.48 Å R-free 0.209
6HDQ N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH : 8-(((1R,2R,3R,5S)-2-(2-(4,4-difluorocyclohexyl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one Deposited 2018-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 FZE 8-(((1R,2R,3R,5S)-2-(2-(4,4-difluorocyclohexyl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；20% PEG6K, 0.2M LiCl, 0.1M tris pH8 at 20C
Resolution 1.70 Å R-free 0.241
6HOV Crystal Structure of BRD4 first bromodomain in complex with ferulic acid Deposited 2018-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain (residues 44-168)
Mutation：First two residues SM derive from the expression tag EDO 1,2-ETHANEDIOL × 2 FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol
Resolution 1.85 Å R-free 0.216
6I7X Crystal Structure of the first bromodomain of BRD4 in complex with RT53 Deposited 2018-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 H7B 2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-1-[4-(dimethylamino)piperidin-1-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 8.5 0.02M sodium/potassium phosphate
Resolution 1.20 Å R-free 0.137
6I7Y Crystal Structure of the first bromodomain of BRD4 in complex with RT56 Deposited 2018-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 H7E [1-[4-[2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]ethanoylamino]phenyl]piperidin-4-yl]-trimethyl-azanium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 7.5 0.2M sodium sulfate
Resolution 1.00 Å R-free 0.131
6IN1 Crystal structure of the first bromodomain of BRD4 in complex with 18-Crown-6 Deposited 2018-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded LOC N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide × 1 O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；4 M sodium formate, 0.1 M Tris-HCl pH 8.0
Resolution 1.50 Å R-free 0.188
6JI3 BRD4-BD1 bound with ligand 103 Deposited 2019-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded BW6 (3~{R})-4-cyclopropyl-1,3-dimethyl-6-(1~{H}-pyrrol-2-yl)-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；3.2-3.8 M NAFORMATE,10% GLYCEROL
Resolution 2.20 Å R-free 0.258
6JI4 brd4-bd1 bound with ligand 138 Deposited 2019-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded BOF (3R)-4-cyclopropyl-1,3-dimethyl-6-[5-methyl-4-(4-methylphenyl)-4H-1,2,4-triazol-3-yl]-3,4-dihydroquinoxalin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；3.2-3.8 M NAFORMATE,10% GLYCEROL
Resolution 1.60 Å R-free 0.231
6JI5 brd4-bd1 bound with ligand 167 Deposited 2019-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded BQ0 (3R)-4-cyclopentyl-6-[1-(2,4-dimethylphenyl)-3-(4-methylpiperazine-1-carbonyl)-1H-1,2,4-triazol-5-yl]-1,3-dimethyl-3,4-dihydroquinoxalin-2(1H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；293 K；3.2-3.8 M NAFORMATE,10% GLYCEROL
Resolution 2.00 Å R-free 0.262
6JJ3 BRD4 in complex with 138A Deposited 2019-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded BS6 2-methoxy-N-[2-methyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0M HCOONa
Resolution 1.72 Å R-free 0.305
6JJ5 BRD4 in complex with 259 Deposited 2019-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded C6X 3-((1-methyl-2-oxo-1,2,2a1,5a-tetrahydro-6H-pyrido[3',2':6,7]azepino[4,3,2-cd]isoindol-6-yl)methyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0M HCOONa
Resolution 1.20 Å R-free 0.203
6JJ6 BRD4 in complex with 500 Deposited 2019-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded C89 1-methyl-6-(3-(4-methylpiperazine-1-carbonyl)benzyl)-1,2a1,5a,6-tetrahydro-2H-pyrido[3',2':6,7]azepino[4,3,2-cd]isoindol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0M HCOONa
Resolution 1.40 Å R-free 0.201
6JJB BRD4 in complex with ZZM1 Deposited 2019-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded BT0 2-methoxy-N-(1-methyl-2-oxidanylidene-benzo[cd]indol-6-yl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0M HCOONa
Resolution 1.51 Å R-free 0.228
6KEC Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 4-ethoxy-5,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded D9C 4-ethoxy-5,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one × 1 FMT FORMIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6 M sodium formate, 10% glycerol
Resolution 1.35 Å R-free 0.201
6KED BRD4 Bromodomain1 with an inhibitor Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded D7R 6-[2-[2,4-bis(fluoranyl)phenoxy]-5-(methylsulfonylmethyl)pyridin-3-yl]-8-methyl-2H-pyrrolo[1,2-d][1,2,4]triazin-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M Sodium formate, 15% glycerol
Resolution 2.55 Å R-free 0.379
6KEE Crystal structure of BRD4 Bromodomain1 with an inhibitor Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded D7U 6-[2-[2,4-bis(fluoranyl)phenoxy]-5-(methylsulfonylmethyl)pyridin-3-yl]-8-methyl-2H-pyrrolo[1,2-a]pyrazin-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M Sodium Formate, 15% glycerol
Resolution 2.12 Å R-free 0.274
6KEF BRD4 Bromodomain1 with an inhibitor Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded D7X N-[3-(8-methyl-1-oxidanylidene-2H-pyrrolo[1,2-a]pyrazin-6-yl)-4-phenoxy-phenyl]methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；4M Sodium Formate, 15% glycerol
Resolution 2.44 Å R-free 0.345
6KEG BRD4 Bromodomain1 with an inhibitor Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded D89 6-[2-[2,4-bis(fluoranyl)phenoxy]-5-(ethylsulfonylmethyl)pyridin-3-yl]-8-methyl-4H-pyrrolo[1,2-a]pyrazin-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；4M sodium formate, 15% glycerol
Resolution 2.23 Å R-free 0.330
6KEH Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded FMT FORMIC ACID × 4 D6R 6,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6 M Sodium formate, 10% Glycerol
Resolution 1.55 Å R-free 0.230
6KEI Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded D6U 16-methoxy-11-methyl-6-[(pyridin-2-yl)methoxy]-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6 M Sodium formate, 10% Glycerol
Resolution 1.45 Å R-free 0.231
6KEJ Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-[2-(diethylamino)ethoxy]-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded D7F 6-[2-(diethylamino)ethoxy]-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6 M Sodium Formate, 10% Glycerol
Resolution 1.85 Å R-free 0.242
6KEK Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-hydroxy-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one Deposited 2019-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded FMT FORMIC ACID × 7 D7L 6-hydroxy-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6 M sodium formate, 10% glycerol
Resolution 1.55 Å R-free 0.232
6KO2 Crystal Structure of BRD4-Brmo2 in complex with H2A.ZK4acK7ac peptide Deposited 2019-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 351–457（107 aa） Fragment：Bromo2 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.1M Amino acids, 0.1M Buffer System 3, 50% v/v Precipitant Mix 4 (morpheus)
Resolution 1.50 Å R-free 0.185
6LG4 crystal structure of the first bromodomain of human BRD4 in complex with compound BDF-1024 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded EC0 7-chloranyl-5-nitro-quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.85 Å R-free 0.238
6LG5 Crystal Structure of the first bromodomain of human BRD4 in complex with compound BDF-1038 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded EC3 1-[(5-chloranyl-8-oxidanyl-quinolin-7-yl)methyl]pyrrolidin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.83 Å R-free 0.202
6LG6 Crystal Structure of the first bromodomain of human BRD4 in complex with compound BDF-1021 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded EC9 N-[8-oxidanyl-4-(pyridin-2-ylamino)quinolin-2-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.98 Å R-free 0.278
6LG7 Crystal Structure of the first bromodomain of human BRD4 in complex with compound BDF-2030 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded ECF 2-azanyl-6-fluoranyl-4-imidazol-1-yl-quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.83 Å R-free 0.235
6LG8 crystal structure of the first bromodomain of human BRD4 in complex with compound BDF-2138 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded ECR 2-azanyl-5-fluoranyl-4-imidazol-1-yl-quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.58 Å R-free 0.197
6LG9 crystal structure of the first bromodomain of human BRD4 in complex with compound BDF-2143 Deposited 2019-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded ECU 2-azanyl-7-bromanyl-4-imidazol-1-yl-quinolin-8-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；10-15% glycerol, 4M sodium formate
Resolution 1.81 Å R-free 0.243
6LIH BRD4 BD1 bound with compound 10 Deposited 2019-12-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded EDF (3~{R})-1,3-dimethyl-6-[(4-phenylpyrimidin-2-yl)amino]-4-propan-2-yl-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；289 K；protein concentration 10 mg/ML, 2.8-3.8M sodium formate, 10% glycerol
Resolution 1.62 Å R-free 0.212
6LIM BRD4-BD1 bound with compound 40 Deposited 2019-12-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded EE9 (3~{R})-6-[(4-isoquinolin-4-ylpyrimidin-2-yl)amino]-1,3-dimethyl-4-propan-2-yl-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7；289 K；10mg/ml, 2.8-3.8M sodium formate, glycerol 10%
Resolution 1.76 Å R-free 0.235
6MAU Crystal structure of human BRD4(1) in complex with CN210 (compound 19) Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–170（127 aa）
Not recorded JBS 1-(4-{6-(3,5-dimethyl-1,2-oxazol-4-yl)-4-[(3S)-3-phenylmorpholin-4-yl]quinazolin-2-yl}-1H-pyrazol-1-yl)-2-methylpropan-2-ol × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；276 K；1.4 M Sodium/Potassium Phosphate pH 8.2
Resolution 2.11 Å R-free 0.253
6MH1 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH HU-10, A 1,4,5-Trisubstituted Imidazole Analogue Deposited 2018-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain, residues 44-168
Not recorded JQP N-(3,5-dimethylphenyl)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidin-2-amine × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM HU-10
Resolution 1.60 Å R-free 0.202
6MH1 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH HU-10, A 1,4,5-Trisubstituted Imidazole Analogue Deposited 2018-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：Bromo 1 domain, residues 44-168
Not recorded JQP N-(3,5-dimethylphenyl)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidin-2-amine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 MG/ML BRD4, 5MM HEPES PH 7.5, 50MM SODIUM CHLORIDE, 0.5MM DTT, 50MM TRIS PH8.5, 0.1M AMMONIUM, SULFATE, 12.5% PEG 3,350, 10% DMSO, 1 MM HU-10
Resolution 1.60 Å R-free 0.202
6MH7 Crystal structure of the first bromodomain of human BRD4 in complex with SKT-68, a 1,4,5-trisubstituted imidazole analogue Deposited 2018-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded JQY N-(3,4-dimethylphenyl)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidin-2-amine × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL BRD4, 5 mM HEPES, pH 7.5, 50 mM sodium chloride, 0.5 mM DTT, 50 mM Tris, pH 8.5, 0.1 M ammonium sulfate, 12.5% PEG3350, 10% DMSO, 1 mM SKT-68
Resolution 1.74 Å R-free 0.185
6MH7 Crystal structure of the first bromodomain of human BRD4 in complex with SKT-68, a 1,4,5-trisubstituted imidazole analogue Deposited 2018-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded JQY N-(3,4-dimethylphenyl)-4-[4-(4-fluorophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]pyrimidin-2-amine × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；12.5 mg/mL BRD4, 5 mM HEPES, pH 7.5, 50 mM sodium chloride, 0.5 mM DTT, 50 mM Tris, pH 8.5, 0.1 M ammonium sulfate, 12.5% PEG3350, 10% DMSO, 1 mM SKT-68
Resolution 1.74 Å R-free 0.185
6MNL NMR solution structures of second bromodomain of BRD4 with FOXO3a peptide Deposited 2018-10-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 333–460（128 aa） Fragment：Bromo 2 domain, residues 333-460
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Pressure 1
NMR sample composition 100 mM sodium chloride, 10 mM sodium phosphate, 2 mM [U-100% 2H] DTT, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 100 mM sodium chloride, 10 mM sodium phosphate, 2 mM [U-100% 2H] DTT, 100% D2O | 100% D2O
Resolution not provided
6P05 Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with compound 27 Deposited 2019-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded GOL GLYCEROL × 2 YF2 N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(1-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-3-yl)-1H-indol-4-yl}ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；16-18% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M LiSO4
Resolution 1.54 Å R-free 0.180
6PRT Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 10 (methyl [(3R)-1-methyl-5-oxopyrrolidin-3-yl]acetate) Deposited 2019-07-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded OWA methyl [(3R)-1-methyl-5-oxopyrrolidin-3-yl]acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.30 Å R-free 0.166
6PS9 Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 17 (5-{2-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]ethyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one) Deposited 2019-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded Y17 5-{2-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]ethyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.21 Å R-free 0.164
6PSB Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 18 (5-{[(3R)-1-methyl-5-oxopyrrolidin-3-yl]methyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one) Deposited 2019-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded Y18 5-{[(3R)-1-methyl-5-oxopyrrolidin-3-yl]methyl}-2,3,4,5-tetrahydro-1H-pyrido[4,3-b]indol-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.59 Å R-free 0.209
6Q3Y Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16i Deposited 2018-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 HG5 (7~{R})-2-[[2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl]amino]-7-ethyl-5-methyl-8-(phenylmethyl)-7~{H}-pteridin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30% pentaerythritol ethoxylate 15/4, 0.05 ammonium sulfate, 0.1M bis-tris pH6.5
Resolution 1.20 Å R-free 0.176
6Q3Y Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16i Deposited 2018-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 HG5 (7~{R})-2-[[2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl]amino]-7-ethyl-5-methyl-8-(phenylmethyl)-7~{H}-pteridin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；30% pentaerythritol ethoxylate 15/4, 0.05 ammonium sulfate, 0.1M bis-tris pH6.5
Resolution 1.20 Å R-free 0.176
6Q3Z Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16k Deposited 2018-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded HG8 (7~{R})-2-[[2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl]amino]-7-ethyl-5-methyl-8-[(4-methylthiophen-2-yl)methyl]-7~{H}-pteridin-6-one × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH6.5
Resolution 2.00 Å R-free 0.231
6Q3Z Crystal structure of the first bromodomain of human BRD4 in complex with the inhibitor 16k Deposited 2018-12-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded HG8 (7~{R})-2-[[2-ethoxy-4-(1-methylpiperidin-4-yl)phenyl]amino]-7-ethyl-5-methyl-8-[(4-methylthiophen-2-yl)methyl]-7~{H}-pteridin-6-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；25% PEG3350, 0.2M ammonium sulfate, 0.1M bis-tris pH6.5
Resolution 2.00 Å R-free 0.231
6RWJ Crystal Structure of BRD4(1) bound to inhibitor BUG0 (6) Deposited 2019-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：FIRST BROMODOMAIN (UNP RESIDUES 44-168)
Not recorded KLK ~{N},3-dimethyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；TRIS, PEG3350, NaCl
Resolution 1.40 Å R-free 0.181
6S25 Crystal Structure of the first bromodomain of BRD4 in complex with a benzodiazepine ligand Deposited 2019-06-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 KSZ ~{tert}-butyl ~{N}-[3-[2-[(4~{S})-6-(4-chlorophenyl)-8-methoxy-1-methyl-4~{H}-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]ethanoylamino]propyl]carbamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG6000 10% ethylene glycol 0.2M lithium chloride
Resolution 1.10 Å R-free 0.145
6S4B Crystal Structure of BRD4(1) bound to inhibitor BUX1 (8) Deposited 2019-06-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded BU3 (R,R)-2,3-BUTANEDIOL × 1 KUH ~{N}-[5-(diethylsulfamoyl)-2-methoxy-phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG3350, NaCl, CaCl2, HEPES
Resolution 1.60 Å R-free 0.195
6S6K Crystal Structure of BRD4(1) bound to inhibitor BUX2 (9) Deposited 2019-07-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded KXK ~{N}-[5-(azepan-1-ylsulfonyl)-2-methoxy-phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 BU3 (R,R)-2,3-BUTANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG3350, NaCl
Resolution 1.40 Å R-free 0.158
6SA2 Crystal Structure of BRD4(1) bound to inhibitor BUX3 (10) Deposited 2019-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded BU3 (R,R)-2,3-BUTANEDIOL × 2 L25 ~{N}-(2-methoxy-5-morpholin-4-ylsulfonyl-phenyl)-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；MMW PEG, NaCl
Resolution 1.50 Å R-free 0.185
6SA3 Crystal Structure of BRD4(1) bound to inhibitor BUX4 (13) Deposited 2019-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded L2N ~{N}-[2-methoxy-5-(4-methylpiperazin-1-yl)sulfonyl-phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NaCl, MMW PEG
Resolution 1.80 Å R-free 0.231
6SAH Crystal Structure of BRD4(1) bound to inhibitor BUX5 (11) Deposited 2019-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded L2W ~{N}-(2-methoxy-5-piperidin-1-ylsulfonyl-phenyl)-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Index D6, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.50 Å R-free 0.169
6SAJ Crystal Structure of BRD4(1) bound to inhibitor BUX6 (12) Deposited 2019-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded BU3 (R,R)-2,3-BUTANEDIOL × 3 L2Z ~{N}-[2-methoxy-5-(2-oxa-6-azaspiro[3.3]heptan-6-ylsulfonyl)phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, PEG3350
Resolution 1.50 Å R-free 0.180
6SB8 Crystal Structure of BRD4(1) bound to inhibitor BUX14 (7) Deposited 2019-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded L45 ~{N}-[5-(diethylsulfamoyl)-2-oxidanyl-phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NaCl, PEG3350, HEPES
Resolution 1.50 Å R-free 0.207
6SE4 Crystal Structure of the first bromodomain of human BRD4 in complex with (+)-JD1, an Organometallic BET Bromodomain Inhibitor Deposited 2019-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 L8W (+)-JD1 × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；60% MPD, 0.1M MIB pH 8.0
Resolution 1.38 Å R-free 0.179
6SIS Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB Deposited 2019-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 333–460（128 aa）
Not recorded LFE ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% (w/v) PEG 8000, 0.1 M Tris-HCl (pH 7.5) and 0.1 M MgCl2
Resolution 3.50 Å R-free 0.247
6SIS Crystal structure of macrocyclic PROTAC 1 in complex with the second bromodomain of human Brd4 and pVHL:ElonginC:ElonginB Deposited 2019-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 333–460（128 aa）
Not recorded LFE ~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；10% (w/v) PEG 8000, 0.1 M Tris-HCl (pH 7.5) and 0.1 M MgCl2
Resolution 3.50 Å R-free 0.247
6SWN N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD1 (GSK778) Deposited 2019-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded GLU GLUTAMIC ACID × 1 LWB 4-[2-(methoxymethyl)-1-[(1~{R})-1-phenylethyl]-8-[[(3~{S})-pyrrolidin-3-yl]methoxy]imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；20% PEG3350, 0.2M NaI, 0.1M BTP, 20C
Resolution 1.28 Å R-free 0.212
6SWQ N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD2 (GSK046) Deposited 2019-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 LW5 4-acetamido-3-fluoranyl-~{N}-(4-oxidanylcyclohexyl)-5-[(1~{S})-1-phenylethoxy]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25%w/v PEG1500, 0.1M SPG buffer, pH 6
Resolution 1.60 Å R-free 0.184
6TPX N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-((1-acetylpiperidin-4-yl)methyl)-2-(4-hydroxy-3,5-dimethylphenyl)-N-methyl-1H-benzo[d]imidazole-5-carboxamide Deposited 2019-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded NUW 2-(3,5-dimethyl-4-oxidanyl-phenyl)-1-[(1-ethanoylpiperidin-4-yl)methyl]-~{N}-methyl-benzimidazole-5-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG6000, 0.2M NH4Cl, 0.1M tris pH8
Resolution 1.48 Å R-free 0.181
6TPY N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1,3-dimethyl-5-(1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one Deposited 2019-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 NUB 1,3-dimethyl-5-[1-(oxan-4-ylmethyl)benzimidazol-2-yl]pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M BTP pH8.5, 20% PEG3350
Resolution 1.80 Å R-free 0.255
6TPZ N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 5-(1-(1,3-dimethoxypropan-2-yl)-5-morpholino-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one Deposited 2019-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 NV2 5-[1-(1,3-dimethoxypropan-2-yl)-5-morpholin-4-yl-benzimidazol-2-yl]-1,3-dimethyl-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；of 0.1 PCTP pH 8.0, 25% v/v PEG1500
Resolution 1.30 Å R-free 0.218
6U0D Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZL0590 Deposited 2019-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 1 POJ N-[4-({(2S)-2-[(morpholin-4-yl)methyl]pyrrolidin-1-yl}sulfonyl)phenyl]-N'-[4-(trifluoromethyl)phenyl]urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM HEPES, 15% PEG 3350 at pH 7.5
Resolution 1.43 Å R-free 0.223
6U6K BRD4-BD1 in complex with the cyclic peptide 3.1_3 Deposited 2019-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MMT 7.0 25 % w/v PEG 1500
Resolution 1.70 Å R-free 0.218
6U6L BRD4-BD2 in complex with the cyclic peptide 3.1_2 Deposited 2019-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 347–464（118 aa）
Not recorded NH2 AMINO GROUP × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG3350
Resolution 2.60 Å R-free 0.242
6U72 BRD4-BD1 in complex with the cyclic peptide 3.1_2_AcK5toA Deposited 2019-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa）
Chain B 42–168（127 aa）
Not recorded NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；5% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 10,000
Resolution 2.30 Å R-free 0.266
6U74 BRD4-BD1 in complex with the cyclic peptide 3.1_2 Deposited 2019-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa）
Chain C 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane 7.5, 20 % w/v PEG 3350
Resolution 1.85 Å R-free 0.323
6U74 BRD4-BD1 in complex with the cyclic peptide 3.1_2 Deposited 2019-08-31 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 42–168（127 aa）
Chain D 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium malonate dibasic monohydrate, 0.1 M Bis-Tris propane 7.5, 20 % w/v PEG 3350
Resolution 1.85 Å R-free 0.323
6U8G BRD4-BD2 in complex with the cyclic peptide 3.1_2_AcK7toA Deposited 2019-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa）
Chain C 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Ammonium sulfate, 0.1 M BIS-Tris pH 5.5, 1 % w/v PEG 3350
Resolution 2.60 Å R-free 0.296
6U8G BRD4-BD2 in complex with the cyclic peptide 3.1_2_AcK7toA Deposited 2019-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 42–168（127 aa）
Chain D 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M Ammonium sulfate, 0.1 M BIS-Tris pH 5.5, 1 % w/v PEG 3350
Resolution 2.60 Å R-free 0.296
6U8I BRD4-BD2 in complex with the cyclic peptide 3.2_2 Deposited 2019-09-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 347–464（118 aa）
Not recorded NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium iodide, 0.1 M Bis-Tris propane 7.5, 20 % w/v PEG 3350
Resolution 2.50 Å R-free 0.239
6U8M BRD4-BD1 in complex with the cyclic peptide 3.2_1 Deposited 2019-09-05 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa）
Chain B 42–168（127 aa）
Not recorded NH2 AMINO GROUP × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2% v/v 1,4-Dioxane, 0.1 M Tris pH 8.0, 15% w/v Polyethylene glycol 3,350
Resolution 1.95 Å R-free 0.200
6ULS BRD4-BD1 in complex with the a diacetylated-E2F1 peptide Deposited 2019-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M MMT pH 7.0, 25% w/v PEG 1500
Resolution 1.50 Å R-free 0.204
6ULV BRD4-BD1 in complex with the cyclic peptide 4.2_1 Deposited 2019-10-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 42–168（127 aa） Fragment：first bromodomain
Chain C 42–168（127 aa） Fragment：first bromodomain
Not recorded IOD IODIDE ION × 4 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Sodium Iodide (150-250mM), PEG 3350 (15-25%) and 100mM Bis Tris Propane
Resolution 2.20 Å R-free 0.238
6ULV BRD4-BD1 in complex with the cyclic peptide 4.2_1 Deposited 2019-10-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 42–168（127 aa） Fragment：first bromodomain
Chain D 42–168（127 aa） Fragment：first bromodomain
Not recorded IOD IODIDE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；Sodium Iodide (150-250mM), PEG 3350 (15-25%) and 100mM Bis Tris Propane
Resolution 2.20 Å R-free 0.238
6UVJ Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor Deposited 2019-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 QJ1 methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M bis-tris propane, 20 % PEG 3350
Resolution 1.38 Å R-free 0.197
6UVM Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor Deposited 2019-11-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded QJA 1-[(7S)-7-(thiophen-2-yl)-6,7-dihydro-1,4-thiazepin-4(5H)-yl]ethan-1-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；295 K；0.1 M bis-tris propane, 20% ethylene glycol, and 20% PEG3350
Resolution 1.51 Å R-free 0.218
6UWU Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZL0516 Deposited 2019-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 QKP 2-{4-[(2R)-2-hydroxy-3-(4-methylpiperazin-1-yl)propoxy]-3,5-dimethylphenyl}-5,7-dimethoxy-4H-1-benzopyran-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100 mM sodium sulfate, 10% (v/v) ethylene glycol and 18% (w/v) PEG 3350
Resolution 2.00 Å R-free 0.261
6UWX Cocrystal of BRD4(D1) with a ethyl carbamate thiazepane inhibitor Deposited 2019-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 QKD ethyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1 M bis-tris propane, 20 % PEG 3350
Resolution 1.31 Å R-free 0.192
6V0U Crystal structure of the first bromodomain (BD1) of human BRD4 bound to bromosporine Deposited 2019-11-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded BMF Bromosporine × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5), and 25% PEG 3350
Resolution 1.40 Å R-free 0.185
6V1K Crystal structure of the first bromodomain (BD1) of human BRD4 bound to BI7273 Deposited 2019-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5SW 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5), and 25% PEG 3350
Resolution 1.75 Å R-free 0.214
6V1L Crystal structure of the first bromodomain (BD1) of human BRD4 bound to BI9564 Deposited 2019-11-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5U6 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5), and 25% PEG 3350
Resolution 2.10 Å R-free 0.224
6V1U Crystal structure of the first bromodomain (BD1) of human BRD4 bound to TP-472 Deposited 2019-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded QMG 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5), and 25% PEG 3350
Resolution 1.73 Å R-free 0.200
6VIW BRD4_Bromodomain1 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0 M Na Formate, 0.1M Tris pH 8.5
Resolution 2.43 Å R-free 0.232
6VIW BRD4_Bromodomain1 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0 M Na Formate, 0.1M Tris pH 8.5
Resolution 2.43 Å R-free 0.232
6VIW BRD4_Bromodomain1 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0 M Na Formate, 0.1M Tris pH 8.5
Resolution 2.43 Å R-free 0.232
6VIX BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：Bromodomain 2
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；25% PEG 3350, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5
Resolution 2.12 Å R-free 0.230
6VIX BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：Bromodomain 2
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；25% PEG 3350, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5
Resolution 2.12 Å R-free 0.230
6VIX BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 352–457（106 aa） Fragment：Bromodomain 2
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；25% PEG 3350, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5
Resolution 2.12 Å R-free 0.230
6VIX BRD4_Bromodomain2 complex with pyrrolopyridone compound 18 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 352–457（106 aa） Fragment：Bromodomain 2
Not recorded QYV 4-[2-(2,4-difluorophenoxy)-5-(methylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；25% PEG 3350, 0.2M AmSO4, 0.1M Na Cacodylate, pH 5.5
Resolution 2.12 Å R-free 0.230
6VIZ BRD4_Bromodomain1 complex with pyrrolopyridone compound 27 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYY 4-[2-(2,6-dimethylphenoxy)-5-(ethylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0M Na Formate, 0.1M Bis-Tris Propane, pH 7.0
Resolution 2.39 Å R-free 0.217
6VIZ BRD4_Bromodomain1 complex with pyrrolopyridone compound 27 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYY 4-[2-(2,6-dimethylphenoxy)-5-(ethylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0M Na Formate, 0.1M Bis-Tris Propane, pH 7.0
Resolution 2.39 Å R-free 0.217
6VIZ BRD4_Bromodomain1 complex with pyrrolopyridone compound 27 Deposited 2020-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 57–168（112 aa） Fragment：Bromodomain 1
Not recorded QYY 4-[2-(2,6-dimethylphenoxy)-5-(ethylsulfonyl)phenyl]-N-ethyl-6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；2.0M Na Formate, 0.1M Bis-Tris Propane, pH 7.0
Resolution 2.39 Å R-free 0.217
6VUB Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 5 (1-methyl-4-phenylpyrrolidin-2-one) Deposited 2020-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded RLG (4R)-1-methyl-4-phenylpyrrolidin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.50 Å R-free 0.177
6VUC Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 7b (1-methyl-4-(4-(piperidin-1-ylsulfonyl)phenyl)pyrrolidin-2-one) Deposited 2020-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded RLS (4R)-1-methyl-4-{4-[(piperidin-1-yl)sulfonyl]phenyl}pyrrolidin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.55 Å R-free 0.211
6VUF Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 7h (4-(1-methyl-5-oxopyrrolidin-3-yl)-N-propylbenzenesulfonamide) Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded RLV 4-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]-N-propylbenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.59 Å R-free 0.269
6VUF Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 7h (4-(1-methyl-5-oxopyrrolidin-3-yl)-N-propylbenzenesulfonamide) Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded RLV 4-[(3R)-1-methyl-5-oxopyrrolidin-3-yl]-N-propylbenzene-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.59 Å R-free 0.269
6VUJ Crystal structure of BRD4 bromodomain 1 with N-methylpyrrolidin-2-one (NMP) derivative 15c (N,N-diethyl-3',4'-dimethoxy-6-(1-methyl-5-oxopyrrolidin-3-yl)-[1,1'-biphenyl]-3-sulfonamide) Deposited 2020-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded NO3 NITRATE ION × 1 RLY N,N-diethyl-3',4'-dimethoxy-6-[(3S)-1-methyl-5-oxopyrrolidin-3-yl][1,1'-biphenyl]-3-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.2 M sodium nitrate, 35% PEG3350, 6% v/v ethylene glycol
Resolution 1.48 Å R-free 0.208
6WGX Cocrystal of BRD4(D1) with a selective inhibitor Deposited 2020-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 U0D 4-(1-{1-[2-(dimethylamino)ethyl]piperidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-5-yl)-N-(3,5-dimethylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol
Resolution 1.53 Å R-free 0.181
6WGX Cocrystal of BRD4(D1) with a selective inhibitor Deposited 2020-04-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 U0D 4-(1-{1-[2-(dimethylamino)ethyl]piperidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-5-yl)-N-(3,5-dimethylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol
Resolution 1.53 Å R-free 0.181
6WVX Crystal structure of the first bromodomain of human BRD4 with benzodiazepine inhibitor Deposited 2020-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded UDV 6'-(4-chlorophenyl)-1'-methyl-8'-(1-methyl-1H-pyrazol-4-yl)spiro[cyclopropane-1,4'-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine] × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.18 M Triammonium Citrate, 20% (w/v) PEG 3350
Resolution 1.55 Å R-free 0.246
6WVX Crystal structure of the first bromodomain of human BRD4 with benzodiazepine inhibitor Deposited 2020-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded UDV 6'-(4-chlorophenyl)-1'-methyl-8'-(1-methyl-1H-pyrazol-4-yl)spiro[cyclopropane-1,4'-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine] × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.18 M Triammonium Citrate, 20% (w/v) PEG 3350
Resolution 1.55 Å R-free 0.246
6WW8 BRD4 Bromodomain 1 in complex with triple CDK4/6-PI3K-BET inhibitor Deposited 2020-05-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–180（138 aa）
Not recorded YR0 7-cyclopentyl-N,N-dimethyl-2-({4-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]phenyl}amino)-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Tris pH 8.5, 25%(w/v) PEG 3350, and 200 mM NH4Cl
Resolution 2.30 Å R-free 0.235
6X7B BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212P Deposited 2020-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–176（133 aa）
Not recorded ZVP 7-[7-oxo-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.2 M NH4Cl, 0.1 M Tris pH 8.5
Resolution 1.95 Å R-free 0.221
6X7B BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212P Deposited 2020-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–176（133 aa）
Not recorded ZVP 7-[7-oxo-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.2 M NH4Cl, 0.1 M Tris pH 8.5
Resolution 1.95 Å R-free 0.221
6X7C BRD4 Bromodomain 1 in complex with multi-action inhibitor SRX3212 Deposited 2020-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–176（133 aa）
Not recorded KV9 7-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；40% PEG 3350, 0.2 M Pottassium thiocyanate pH 7.5, and 4% 1,1,1,3,3,3-Hexafluoro-2-propanol
Resolution 2.70 Å R-free 0.257
6X7D BRD4 Bromodomain 1 in complex with multi-action inhibitor SF2523P Deposited 2020-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–176（133 aa）
Not recorded UT4 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2.5 M Ammonium Sulfate and 0.1 M Tris pH 8.5
Resolution 2.50 Å R-free 0.267
6X7D BRD4 Bromodomain 1 in complex with multi-action inhibitor SF2523P Deposited 2020-05-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–176（133 aa）
Not recorded UT4 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(piperazin-1-yl)-7H-thieno[3,2-b]pyran-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；2.5 M Ammonium Sulfate and 0.1 M Tris pH 8.5
Resolution 2.50 Å R-free 0.267
6XUZ CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 4 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded O1W 6-[1-[(2~{S})-1-methoxypropan-2-yl]-6-[(3~{S})-3-methylmorpholin-4-yl]imidazo[4,5-c]pyridin-2-yl]-3-methyl-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29% PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.07 Å R-free 0.201
6XV3 CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded O2B 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.47 Å R-free 0.290
6XV3 CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded O2B 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.47 Å R-free 0.290
6XV3 CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded O2B 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.47 Å R-free 0.290
6XV3 CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 3 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded O2B 3-methyl-6-[6-[(3~{S})-3-methylmorpholin-4-yl]-1-[(1~{S})-1-phenylethyl]imidazo[4,5-c]pyridin-2-yl]-~{N}-propan-2-yl-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.47 Å R-free 0.290
6XV7 CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 2 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 O2Q ~{N}-[[3,4-bis(fluoranyl)phenyl]methyl]-~{N},3-dimethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.67 Å R-free 0.203
6XVC CRYSTAL STRUCTURE OF BRD4-BD1 WITH COMPOUND 1 Deposited 2020-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 O32 (4~{R})-4-[(1~{R})-1-[7-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-6-yl)quinolin-5-yl]oxyethyl]pyrrolidin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；29 % PEG 3350, 0.2 M disodium malonate, 0.1 M HEPES
Resolution 1.10 Å R-free 0.198
6YIN Crystal structure of the first bromodomain of BRD4 in complex with a benzo-diazepine ligand Deposited 2020-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded OS8 (4~{R})-~{N}-[3-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)propyl]-4-methyl-2-oxidanylidene-1,3,4,5-tetrahydro-1,5-benzodiazepine-6-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；30% PEG1000 0.1M MIB pH 7.0
Resolution 1.53 Å R-free 0.245
6YQN Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW9 Deposited 2020-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 P8T ~{N}-(2-aminophenyl)-4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]t rideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW12 in DMSO added to give a final inhibitor concentration 1.5 mM. Reservoir buffer: 24% PEG 3350, 0.1 M sodium formate, 15% ethylene glycol and 0.1 M bis-Tris-propane pH 7.3. Ratio protein/reservoir solution = 2:1
Resolution 1.05 Å R-free 0.176
6YQO Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW12 Deposited 2020-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 P8Q (S)-N1-(4-(2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetamido)phenyl)-N8-hydroxyoctanediamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW12 in DMSO added to give a final inhibitor concentration 1.5 mM. Reservoir buffer: 24% PEG 3350, 0.1 M sodium formate, 15% ethylene glycol and 0.1 M bis-Tris-propane pH 7.3. Ratio protein/reservoir solution = 2:1
Resolution 1.07 Å R-free 0.174
6YQP Crystal structure of the first bromodomain of human BRD4 in complex with the dual inhibitor TW22 Deposited 2020-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 P8N (~{E})-3-[4-[[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6 ),4,7,10,12-pentaen-9-yl]ethanoylamino]methyl]phenyl]-~{N}-oxidanyl-prop-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/ml in 10 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM TCEP, and 5% glycerol. 50 mM stock solution of TW22 in DMSO added to give a final inhibitor concentration 1.5 mM. Reservoir buffer: 24% PEG 3350, 0.2 M sodium formate, 15 % ethylene glycol and 0.1 M bis-Tris-propane pH 7.9
Resolution 1.25 Å R-free 0.193
6YQZ N-terminal domain of BRD4 with biphenyl-methyamino-dimethylpyridazinone Deposited 2020-04-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded P8W 2,4-dimethyl-5-[(2-phenylphenyl)methylamino]pyridazin-3-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；20%w/v PEG 3350, 0.2M sodium sulphate,0.1M bis-tris-propane (pH 6.5)
Resolution 1.39 Å R-free 0.204
6Z7G N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH N-(2-(1H-imidazol-4-yl)ethyl)-4-acetamido-3-(benzyloxy)benzamide Deposited 2020-05-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded QB5 N-(2-(1H-imidazol-4-yl)ethyl)-4-acetamido-3-(benzyloxy)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.2M BTP pH 6.5, 20% PEG3350, 0.2M NaKtartrate
Resolution 1.59 Å R-free 0.218
6Z7L N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with GSK789 Deposited 2020-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded QAN (3~{R},4~{R})-~{N}-cyclohexyl-4-[[5-(furan-2-yl)-3-methyl-2-oxidanylidene-1~{H}-1,7-naphthyridin-8-yl]amino]-1-methyl-piperidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES pH 6.5, 15% v/v PEG400
Resolution 1.62 Å R-free 0.225
6Z7M N-TERMINAL BROMODOMAIN OF HUMAN BRD4 (3R,4R)-N-cyclohexyl-4-((3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)amino)piperidine-3-carboxamide Deposited 2020-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded QAZ (3R,4R)-N-cyclohexyl-4-((3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)amino)piperidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG6K
Resolution 1.26 Å R-free 0.214
6ZB3 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK620 Deposited 2020-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 1PE PENTAETHYLENE GLYCOL × 1 QCZ ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；30%w/v PEG3350, 0.1M NaAc, 0.1M MES, pH 6.5
Resolution 1.42 Å R-free 0.182
6ZCI Crystal structure of BRD4-BD1 in complex with NVS-BET-1 Deposited 2020-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded QFN (4~{R})-4-(4-chlorophenyl)-1-cyclopropyl-5-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)-3-methyl-4~{H}-pyrrolo[3,4-c]pyrazol-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；20% PEG 3350, 200 mM Sodium Malonate pH 5.0
Resolution 1.98 Å R-free 0.274
6ZED CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F1 Deposited 2020-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded QGN 4,5-dimethyl-1~{H}-pyrazolo[3,4-c]pyridazin-3-amine × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1M bis-tris-propane pH 6.5, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Resolution 1.08 Å R-free 0.143
6ZEL CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5 Deposited 2020-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 QGQ 3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Resolution 1.12 Å R-free 0.147
6ZF9 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound SSR4 Deposited 2020-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 QHE 3-ethyl-5-phenyl-[1,3]thiazolo[2,3-c][1,2,4]triazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；20% w/v MMW PgSm, 100mM MES pH 6, 150 mM Ammonium nitrate, 5% ethylene glycol
Resolution 1.20 Å R-free 0.148
7A9U N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 3-(3-(but-3-yn-1-yl)-3H-diazirin-3-yl)-N-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-8-yl)propanamide Deposited 2020-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded R5W 3-(3-(but-3-yn-1-yl)-3H-diazirin-3-yl)-N-(3-methyl-[1,2,4]triazolo[4,3-a]pyridin-8-yl)propanamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；20% PEG 3350 0.2M NaBr
Resolution 1.44 Å R-free 0.210
7AJN Crystal Structure of the first bromodomain of BRD4 in complex with a BzD ligand Deposited 2020-09-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded RGW ~{N}-(1-adamantylmethyl)-2-[(7~{R},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；30% PEG1000 0.1M MIB pH 7.0
Resolution 1.48 Å R-free 0.190
7AQT NMR2 structure of BRD4-BD2 in complex with iBET-762 Deposited 2020-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 351–459（109 aa） Fragment：BRD4-BD2
Not recorded EAM 2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide × 1 SOLUTION NMR
NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 350 uM U-[12C,2H],U-15N,[13C,1H]-Ile-d1, [13C,1H]-Leu-d1/2, [13C,1H]-Val-g1/2 ILV-BRD4-BD2, 50 mM Na2HPO4, 500 uM [U-2H] TCEP, 420 uM iBET-762, 100 % [U-2H] D2O, 100% D2O | 100% D2O
Resolution not provided
7AXR Crystal structure of BRD4(1) bound to the dual BET-HDAC inhibitor LSH24 Deposited 2020-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded S7T 4-acetyl-3-ethyl-N-(3-(3-(hydroxyamino)-3-oxopropyl)phenyl)-5-methyl-1H-pyrrole-2-carboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；35% Tacsimate pH 7.0
Resolution 1.50 Å R-free 0.227
7B1T Crystal structure of BRD4(1) in complex with the inhibitor MPM6 Deposited 2020-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded SOK 3-(5-azanyl-2-chloranyl-phenyl)-1-methyl-4,7-dihydro-2~{H}-cyclohepta[c]pyrrol-8-one × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；HEPES, Sodium citrate tribasic dihydrate
Resolution 1.92 Å R-free 0.189
7C2Z Bromodomain-containing 4 BD1 in complex with 3',4',7,8-Tetrahydroxyflavone Deposited 2020-05-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：BD1 domain
Not recorded SQH 2-[3,4-bis(oxidanyl)phenyl]-7,8-bis(oxidanyl)chromen-4-one × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0M Sodium Formate
Resolution 1.30 Å R-free 0.193
7C6P Bromodomain-containing 4 BD2 in complex with 3',4',7,8- Tetrahydroxyflavonoid Deposited 2020-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa）
Not recorded SQH 2-[3,4-bis(oxidanyl)phenyl]-7,8-bis(oxidanyl)chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；295 K；2. 20 % v/v Polyethylene glycol monomethyl ether 2000, 100 mM Tris PH8.5, 200 mM Trimethylamine N-oxide, 295K
Resolution 1.73 Å R-free 0.222
7DHS Crystal Structure Analysis of the BRD4 Deposited 2020-11-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded H8C 6-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(1R)-1-phenylethyl]benzo[cd]indol-2-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M HEPES, 0.2M NaNO3, 10% ethylene glycol, 20% PEG 3350, pH 6.5
Resolution 1.76 Å R-free 0.253
7EHW BRD4-BD1 in complex with LT-642-602 Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded J4O 1-[4-ethyl-2-methyl-5-(6-morpholin-4-yl-1H-benzimidazol-2-yl)-1H-pyrrol-3-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4 M sodium formate
Resolution 1.65 Å R-free 0.246
7EHY BRD4-BD1 in complex with LT-448-138 Deposited 2021-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded YD8 1-[2,4-dimethyl-5-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-pyrrol-3-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4 M sodium formate
Resolution 1.51 Å R-free 0.207
7EIG BRD4-BD1 in complex with LT-730-903 Deposited 2021-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded N03 1-[5-(5-azanyl-1H-benzimidazol-2-yl)-2-methyl-4-phenyl-1H-pyrrol-3-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4 M sodium formate
Resolution 1.30 Å R-free 0.202
7EIK RD4-BD1 in complex with LT-872-297 Deposited 2021-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded J4R 1-[2-methyl-5-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-4-(1-methylpyrazol-4-yl)-1H-pyrrol-3-yl]ethanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4 M sodium formate
Resolution 1.70 Å R-free 0.258
7EIL BRD4-BD1 in complex with LT-909-110 Deposited 2021-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded 909 N-[4-[4-ethanoyl-5-methyl-2-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-pyrrol-3-yl]phenyl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4M sodium formate
Resolution 1.70 Å R-free 0.212
7FH2 Crystal structure of the first bromodomain of BRD4 in complex with 16D10 Deposited 2021-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded 4JI N-[2-[2-[(E)-3-(2,5-dimethoxyphenyl)prop-2-enoyl]-4,5-dimethoxy-phenyl]ethyl]ethanamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；13.4 mg/mL BRD4-BD1, 0.5 mM 16D10, 20% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate
Resolution 2.49 Å R-free 0.292
7FH2 Crystal structure of the first bromodomain of BRD4 in complex with 16D10 Deposited 2021-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa）
Not recorded 4JI N-[2-[2-[(E)-3-(2,5-dimethoxyphenyl)prop-2-enoyl]-4,5-dimethoxy-phenyl]ethyl]ethanamide × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；13.4 mg/mL BRD4-BD1, 0.5 mM 16D10, 20% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate
Resolution 2.49 Å R-free 0.292
7FH2 Crystal structure of the first bromodomain of BRD4 in complex with 16D10 Deposited 2021-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 42–168（127 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；13.4 mg/mL BRD4-BD1, 0.5 mM 16D10, 20% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate
Resolution 2.49 Å R-free 0.292
7FH2 Crystal structure of the first bromodomain of BRD4 in complex with 16D10 Deposited 2021-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 42–168（127 aa）
Not recorded 4JI N-[2-[2-[(E)-3-(2,5-dimethoxyphenyl)prop-2-enoyl]-4,5-dimethoxy-phenyl]ethyl]ethanamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；13.4 mg/mL BRD4-BD1, 0.5 mM 16D10, 20% PEG 3350, 0.1 M Bis-Tris pH 6.5, 0.2 M ammonium sulfate
Resolution 2.49 Å R-free 0.292
7JKW Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with ZN1-99 Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded VCV N-(6-{5-[(azetidin-3-yl)amino]-1-methyl-6-oxo-1,6-dihydropyridin-3-yl}-1-[1,1-di(pyridin-2-yl)ethyl]-1H-indol-4-yl)ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000
Resolution 1.20 Å R-free 0.185
7JKX Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-6 Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded Y36 N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-[1-methyl-5-(methylamino)-6-oxo-1,6-dihydropyridin-3-yl]-1H-indol-4-yl}ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000
Resolution 1.20 Å R-free 0.209
7JKY Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-126 Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YF6 N-(1-[1,1-di(pyridin-2-yl)ethyl]-6-{1-methyl-6-oxo-5-[(piperidin-4-yl)amino]-1,6-dihydropyridin-3-yl}-1H-indol-4-yl)ethanesulfonamide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000
Resolution 1.16 Å R-free 0.176
7JKZ Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with YF3-126 Deposited 2020-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa）
Not recorded YF6 N-(1-[1,1-di(pyridin-2-yl)ethyl]-6-{1-methyl-6-oxo-5-[(piperidin-4-yl)amino]-1,6-dihydropyridin-3-yl}-1H-indol-4-yl)ethanesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；0.2 M (NH4)2SO4, 0.1M Na cacodylate pH 6.5, 30% PEG 8000
Resolution 2.49 Å R-free 0.212
7K6G Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-IN-1 Deposited 2020-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium sulphate, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.70 Å R-free 0.204
7K6G Crystal structure of the first bromodomain (BD1) of human BRD4 bound to ERK5-IN-1 Deposited 2020-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded VYJ 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium sulphate, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.70 Å R-free 0.204
7K6H Crystal structure of the first bromodomain (BD1) of human BRD4 bound to XMD8-92 Deposited 2020-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 4WG 2-{[2-ethoxy-4-(4-hydroxypiperidin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000
Resolution 1.50 Å R-free 0.190
7KHH Ternary complex of VHL/BRD4-BD1/Compound9 (4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide) Deposited 2020-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 44–168（125 aa）
Not recorded WEP N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；18% w/v PEG 8K, 10% v/v PEG 200, 0.1 M BIS-TRIS propane pH 9.0
Resolution 2.28 Å R-free 0.229
7KHL BRD4-BD1 Compound6 (methyl 4-(3,5-difluoropyridin-2-yl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxylate) Deposited 2020-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded WEM methyl 7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；14% w/v PEG 4K, 0.1 M Tris-HCl pH 8
Resolution 1.29 Å R-free 0.225
7KHL BRD4-BD1 Compound6 (methyl 4-(3,5-difluoropyridin-2-yl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxylate) Deposited 2020-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；14% w/v PEG 4K, 0.1 M Tris-HCl pH 8
Resolution 1.29 Å R-free 0.225
7KO0 Crystal structure of the second bromodomain (BD2) of human BRD4 bound to SG3-179 Deposited 2020-11-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 349–460（112 aa）
Not recorded 5W2 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 20% PEG 3,350
Resolution 1.90 Å R-free 0.199
7L9M Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with bivalent inhibitor GXH-II-083 Deposited 2021-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 XR4 N,N'-[(1,19-dioxo-4,7,10,13,16-pentaoxanonadecane-1,19-diyl)di(piperidine-1,4-diyl)]bis(4-{[4-({3-[(tert-butylsulfonyl)amino]-4-chlorophenyl}amino)-5-methylpyrimidin-2-yl]amino}-2-fluorobenzamide) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulfate, 0.1 M Tris HCl pH 8.5, 25% PEG 3350
Resolution 1.45 Å R-free 0.202
7LA9 Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1 Deposited 2021-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain D 44–168（125 aa）
Not recorded XR7 N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide) × 1 EDO 1,2-ETHANEDIOL × 7 CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate (pH 5.6), 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.208
7LA9 Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1 Deposited 2021-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Chain F 44–168（125 aa）
Not recorded XR7 N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide) × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate (pH 5.6), 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.208
7LA9 Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1 Deposited 2021-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 44–168（125 aa）
Chain E 44–168（125 aa）
Not recorded XR7 N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide) × 1 EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate (pH 5.6), 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.208
7LH8 CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR JJ-II-131 Deposited 2021-01-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded XZG (5R)-1-ethyl-5-(4-methylphenyl)-7-({1-[(4-nitrophenyl)methyl]piperidin-4-yl}methyl)-5,7,8,9-tetrahydro-1H-pyrrolo[3',4':5,6]pyrido[2,3-d]pyrimidine-2,4,6(3H)-trione × 1 EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.75 Å R-free 0.212
7M16 Triazole-based BET family bromodomain inhibitor bound to BRD4(D1) Deposited 2021-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YNS 4-{5-[6-(3,5-dimethylanilino)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidine-1-carboximidamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M sodium nitrate, 20% (v/v) PEG 3350 and 10% ethylene glycol
Resolution 1.42 Å R-free 0.215
7MCE CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-{(7P)-7-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-8-fluoro-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-3-yl}propan-2-ol Deposited 2021-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YWY 2-{(7P)-7-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-8-fluoro-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-3-yl}propan-2-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；60% Tacsimate, pH 7.0
Resolution 1.76 Å R-free 0.288
7MCF CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-6-fluoro-5-[(S)-(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol Deposited 2021-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YX4 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-6-fluoro-5-[(S)-(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM Tris, PH 7.0, 100 mM NaCl, 30%(w/v) PEG 3000
Resolution 2.19 Å R-free 0.234
7MCF CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH 2-{3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-6-fluoro-5-[(S)-(3-fluoropyridin-2-yl)(oxan-4-yl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol Deposited 2021-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100 mM Tris, PH 7.0, 100 mM NaCl, 30%(w/v) PEG 3000
Resolution 2.19 Å R-free 0.234
7MLQ X-ray crystal structure of human BRD4(D1) in complex with 2-(4-{5-[6-(2,5-dibromophenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine (compound 26) Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ZHV 2-(4-{5-[6-(2,5-dibromophenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol
Resolution 1.32 Å R-free 0.162
7MLR X-ray crystal structure of human BRD4(D1) in complex with 2-(4-{5-[6-(3,5-dimethylphenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1- yl}piperidin-1-yl)-N,N-dimethylethan-1-amine (DW34) Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 ZHS 2-(4-{5-[6-(3,5-dimethylphenoxy)pyridin-2-yl]-4-methyl-1H-1,2,3-triazol-1-yl}piperidin-1-yl)-N,N-dimethylethan-1-amine × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol
Resolution 1.20 Å R-free 0.164
7MLS X-ray crystal structure of human BRD4(D1) in complex with 2-(2,5-dibromophenoxy)-6-[4-methyl-1-(piperidin-4-yl)-1H-1,2,3-triazol-5-yl]pyridine (compound 23) Deposited 2021-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZHM 2-(2,5-dibromophenoxy)-6-[4-methyl-1-(piperidin-4-yl)-1H-1,2,3-triazol-5-yl]pyridine × 1 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaI, pH 8.5, Bis-Tris propane, 20% (v/v) PEG 3350, ethylene glycol
Resolution 1.26 Å R-free 0.146
7MR5 Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-052 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded ZMS N,N'-{oxybis[(ethane-2,1-diyl)oxy(1-oxoethane-2,1-diyl)piperidine-1,4-diyl]}bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide} × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4 000
Resolution 1.82 Å R-free 0.212
7MR6 Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-082 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded ZMV N,N'-[(1,16-dioxo-4,7,10,13-tetraoxahexadecane-1,16-diyl)di(piperidine-1,4-diyl)]bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide} × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.85 Å R-free 0.260
7MR7 Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-075 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 ZN1 4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluoro-N-[1-(14-{3-[(2-{3-fluoro-4-[(piperidin-4-yl)carbamoyl]anilino}-5-methylpyrimidin-4-yl)amino]-5-[(2-methylpropane-2-sulfonyl)amino]phenyl}-14-oxo-4,7,10-trioxa-13-azatetradecanan-1-oyl)piperidin-4-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulfate,0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.40 Å R-free 0.194
7MR8 Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-076 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZNJ N-{3-[(2-{3-fluoro-4-[(piperidin-4-yl)carbamoyl]anilino}-5-methylpyrimidin-4-yl)amino]-5-[(2-methylpropane-2-sulfonyl)amino]benzoyl}-L-glutamic acid × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.20 Å R-free 0.177
7MR9 Crystal structure of the first bromodomain (BD1) of human BRD4 bound to NC-II-153 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZMM 2-methyl-4-[3-(2-oxopyrrolidin-1-yl)phenyl]isoquinolin-1(2H)-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.19 Å R-free 0.185
7MRA Crystal structure of the first bromodomain (BD1) of human BRD4 bound to NC-II-259 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZMJ N-[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)phenyl]ethanesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.16 Å R-free 0.186
7MRB Crystal structure of the first bromodomain (BD1) of human BRD4 bound to NC-III-53 Deposited 2021-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded N49 N-[4-(4-chlorophenoxy)-3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)phenyl]ethanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.20 Å R-free 0.190
7O18 N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH I-BET282 Deposited 2021-03-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 UYK (R)-4-(8-methoxy-1-(1-methoxypropan-2-yl)-2-(tetrahydro-2H-pyran-4-yl)-1H-imidazo[4,5-c]quinolin-7-yl)-3,5-dimethylisoxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；200mM CaCl2, 25% OEG4K, 100mM Tris HCl, pH 8.5
Resolution 1.70 Å R-free 0.210
7OEO C-TERMINAL BROMODOMAIN OF HUMAN BRD4 N-(2,2-diphenylethyl)-4-methoxy-3,5-dimethyl-N-(2-(methylamino)-2-oxoethyl)benzamide Deposited 2021-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 347–463（117 aa） Fragment：UNP residues 347-463
Not recorded V9Z N-(2,2-diphenylethyl)-4-methoxy-3,5-dimethyl-N-[2-(methylamino)-2-oxidanylidene-ethyl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Hepes pH7.5 and 20%w/v PEG1500
Resolution 1.51 Å R-free 0.229
7P6V N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 3ag Deposited 2021-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded 5Z4 ethyl 2-(2-(4-azido-N-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)methyl)-2,3,5,6-tetrafluorobenzamido)acetamido)acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；25% w/v PEG1500, 0.1 SPG pH 5.0
Resolution 1.17 Å R-free 0.241
7P6W N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 3bg Deposited 2021-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded 5YY ethyl 2-(2-(4-azido-N-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)methyl)benzamido)acetamido)acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；30%w/v PEG 4K, 0.2M Na Acet, 0.1M TRIS pH 8.5
Resolution 1.31 Å R-free 0.221
7P6Y N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef Deposited 2021-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded 5Z1 4-benzoyl-N-(2-(2-(2-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)(methyl)amino)ethoxy)ethoxy)ethyl)-N-(2-oxo-2-((2-(2-(prop-2-yn-1-yloxy)ethoxy)ethyl)amino)ethyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 sodium citrate pH 5.6, 10% w/v PEG4K, 10% w/v propan-2-ol
Resolution 1.88 Å R-free 0.222
7P6Y N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH compound 5ef Deposited 2021-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 44–168（125 aa）
Not recorded 5Z1 4-benzoyl-N-(2-(2-(2-((2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-benzo[d]imidazol-6-yl)(methyl)amino)ethoxy)ethoxy)ethyl)-N-(2-oxo-2-((2-(2-(prop-2-yn-1-yloxy)ethoxy)ethyl)amino)ethyl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 sodium citrate pH 5.6, 10% w/v PEG4K, 10% w/v propan-2-ol
Resolution 1.88 Å R-free 0.222
7Q3F Bromodomain-containing 4 BD1 in complex with the inhibitor CRCM5484 Deposited 2021-10-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 8M6 2-[[11-ethanoyl-4-(furan-2-ylmethyl)-3-oxidanylidene-8-thia-4,6,11-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),5-trien-5-yl]sulfanyl]-~{N}-(2-methylpyridin-3-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285 K；0.3M NaNO3, 16% PEG3350, 5% Ethylene glycol
Resolution 1.21 Å R-free 0.224
7QDL N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with I-BET567 Deposited 2021-11-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded AKQ (2S,4R)-1-acetyl-4-((5-chloropyrimidin-2-yl)amino)-2-methyl-1,2,3,4-tetrahydroquinoline-6-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Bis-Tris prop pH7.5, 0.02M sodium potassium, 20% v/v PEG3350
Resolution 1.67 Å R-free 0.210
7R5B Crystal structure of BRD4(1) in complex with the inhibitor MPM2 Deposited 2022-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded I5K 1-(3-aminophenyl)-3-methyl-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrol-4-one × 1 BU3 (R,R)-2,3-BUTANEDIOL × 1 DMS DIMETHYL SULFOXIDE × 1 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.77 Å R-free 0.194
7R9C Cocrystal of BRD4(D1) with N,N-dimethyl-2-[(3R)-3-(5-{2-[2-methyl-5-(propan-2-yl)phenoxy]pyrimidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-1-yl)pyrrolidin-1-yl]ethan-1-amine Deposited 2021-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 2IR N,N-dimethyl-2-[(3R)-3-(5-{2-[2-methyl-5-(propan-2-yl)phenoxy]pyrimidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-1-yl)pyrrolidin-1-yl]ethan-1-amine × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.1 M bis-tris propane, 20 % PEG 3350
Resolution 1.50 Å R-free 0.216
7REK Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-086 Deposited 2021-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain residues 44-168
Not recorded R6S N~4~-[1-(tert-butylsulfonyl)-2,3-dihydro-1H-indol-6-yl]-N~2~-[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]-5-methylpyrimidine-2,4-diamine × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.20 Å R-free 0.191
7REK Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-086 Deposited 2021-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：Bromo 1 domain residues 44-168
Not recorded R6S N~4~-[1-(tert-butylsulfonyl)-2,3-dihydro-1H-indol-6-yl]-N~2~-[3-fluoro-4-(1-methylpiperidin-4-yl)phenyl]-5-methylpyrimidine-2,4-diamine × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.20 Å R-free 0.191
7REL Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-060 Deposited 2021-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 4OW N-[2-chloro-5-({2-[3-fluoro-4-(1-methylpiperidin-4-yl)anilino]-5-methylpyrimidin-4-yl}amino)phenyl]-2-methylpropane-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.55 Å R-free 0.191
7REM Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor PN1-050 Deposited 2021-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：Bromo 1 domain residues 44-168
Not recorded 4OF N-[2-chloro-5-({2-[3-fluoro-4-(1-methylpiperidin-4-yl)anilino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)phenyl]-2-methylpropane-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.80 Å R-free 0.226
7RJO Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded NA SODIUM ION × 1 GOL GLYCEROL × 2 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris
Resolution 1.38 Å R-free 0.198
7RJP Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 8 CL CHLORIDE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris
Resolution 1.25 Å R-free 0.174
7RJQ Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with ILF3 Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded NA SODIUM ION × 5 CL CHLORIDE ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；3.0 M sodium chloride, 0.1 M HEPES
Resolution 1.72 Å R-free 0.223
7RJR Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with BCLTF1 Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% w/v PEG4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl
Resolution 1.45 Å R-free 0.207
7RMD Crystal structure of the first bromodomain of human BRD4 in complex with SJ001011461-1 Deposited 2021-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 5Z0 2-[(6S,10R)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(1,3,4-thiadiazol-2-yl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris, pH 6.8, 20% PEG3350, 15% ethylene glycol
Resolution 1.18 Å R-free 0.173
7RN2 Crystal structure of the first bromodomain of human BRD4 in complex with SJ001010551-2 Deposited 2021-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first bromodomain (UNP residues 44-168)
Not recorded EDO 1,2-ETHANEDIOL × 1 5ZQ 2-[(6S,10S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-[(pyridin-2-yl)methyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris, pH 6.8, 20% PEG3350, 15% ethylene glycol
Resolution 1.05 Å R-free 0.184
7RUH Bromodomain-containing protein 4 (BRD4) bromodomain 2 (BD2) complexed with XR844 Deposited 2021-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa） Fragment：bromodomain 2 (UNP residues 333-460)
Non-standard monomer：Yes (specific site not provided by mmCIF) 7QZ N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(5-{[(2-fluorophenyl)carbamoyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-1H-indol-4-yl}-2,2,2-trifluoroethane-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Bis-Tris, pH 6.5, 26% PEG2000 MME
Resolution 1.70 Å R-free 0.218
7RUI Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with XR844 Deposited 2021-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1 (UNP residues 44-168)
Not recorded 7QZ N-{1-[1,1-di(pyridin-2-yl)ethyl]-6-(5-{[(2-fluorophenyl)carbamoyl]amino}-1-methyl-6-oxo-1,6-dihydropyridin-3-yl)-1H-indol-4-yl}-2,2,2-trifluoroethane-1-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；1.6 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 0.1 M sodium chloride
Resolution 1.35 Å R-free 0.190
7RXR Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 7ZB 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG 3350
Resolution 1.41 Å R-free 0.186
7RXR Crystal Structure of BRD4(D1) with 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 7ZB 4-[4-(4-bromophenyl)-1-(piperidin-4-yl)-1H-imidazol-5-yl]-N-(3,5-dimethylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG 3350
Resolution 1.41 Å R-free 0.186
7RXS Crystal of BRD4(D1) with 2-[(3S)-3-{5-[2-(3,5-dimethylphenoxy)pyrimidin-4-yl]-4-(4-iodophenyl)-1H-imidazol-1-yl}pyrrolidin-1-yl]ethan-1-amine Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 7ZT 2-[(3S)-3-{5-[2-(3,5-dimethylphenoxy)pyrimidin-4-yl]-4-(4-iodophenyl)-1H-imidazol-1-yl}pyrrolidin-1-yl]ethan-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG 3350
Resolution 1.43 Å R-free 0.228
7RXT Crystal of BRD4(D1) with 2-[(3R)-3-{5-[2-(3,5-dimethylphenoxy)pyrimidin-4-yl]-4-(4-iodophenyl)-1H-imidazol-1-yl}pyrrolidin-1-yl]ethan-1-amine Deposited 2021-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 7ZK 2-[(3R)-3-{5-[2-(3,5-dimethylphenoxy)pyrimidin-4-yl]-4-(4-iodophenyl)-1H-imidazol-1-yl}pyrrolidin-1-yl]ethan-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；PEG 3350
Resolution 1.68 Å R-free 0.238
7T3F Development of BRD4 inhibitors as arsenicals antidotes Deposited 2021-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded EM0 4-fluoro-3-methyl-N-(3-methyl-2-oxo-1,2,3,4-tetrahydroquinazolin-6-yl)benzene-1-sulfonamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；291 K；20% PEG 3350, 0.2 M ammonium acetate, 0.1 M HEPES, pH7.4
Resolution 1.28 Å R-free 0.145
7TUQ Crystal structure of BRD4 bromodomain 1 in complex with monoacetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.5 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% glycerol
Resolution 2.68 Å R-free 0.276
7TUQ Crystal structure of BRD4 bromodomain 1 in complex with monoacetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.5 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% glycerol
Resolution 2.68 Å R-free 0.276
7TV0 Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.5 M ammonium sulfate, 0.1 mM Tris, pH 8.5, 12% glycerol
Resolution 2.60 Å R-free 0.292
7TV0 Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.5 M ammonium sulfate, 0.1 mM Tris, pH 8.5, 12% glycerol
Resolution 2.60 Å R-free 0.292
7TV0 Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.5 M ammonium sulfate, 0.1 mM Tris, pH 8.5, 12% glycerol
Resolution 2.60 Å R-free 0.292
7TV0 Crystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E Deposited 2022-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 42–180（139 aa） Fragment：BD1 (UNP residues 42-180)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.5 M ammonium sulfate, 0.1 mM Tris, pH 8.5, 12% glycerol
Resolution 2.60 Å R-free 0.292
7UGF First bromodomain of BRD4 liganded with BMS-536924 Deposited 2022-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded N6I (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；0.2M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.45 Å R-free 0.190
7USJ BRD4-BD2 in complex with SF2523 Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：BD2
Not recorded 82V 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；0.1 M HEPES pH 7.5, 28 % w/v PEG 3350
Resolution 2.08 Å R-free 0.265
7USJ BRD4-BD2 in complex with SF2523 Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 352–457（106 aa） Fragment：BD2
Not recorded 82V 3-(2,3-dihydro-1,4-benzodioxin-6-yl)-5-(morpholin-4-yl)-7H-thieno[3,2-b]pyran-7-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；0.1 M HEPES pH 7.5, 28 % w/v PEG 3350
Resolution 2.08 Å R-free 0.265
7USK BRD4-BD2 Ligand free Deposited 2022-04-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 352–457（106 aa） Fragment：BD2
Not recorded EDO 1,2-ETHANEDIOL × 4 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289.15 K；0.1 M HEPES pH 7.5, 28 % w/v PEG 3350
Resolution 1.22 Å R-free 0.232
7UTY First bromodomain of BRD4 liganded with compound 2c Deposited 2022-04-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded OFR prop-2-en-1-yl (5S)-1-ethyl-7-methyl-5-(4-methylphenyl)-2,4-dioxo-1,2,3,4,5,8-hexahydropyrido[2,3-d]pyrimidine-6-carboxylate × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；0.2 M Ammonium sulfate, 0.1 M TRIS pH 8.5, 25% PEG 3350
Resolution 1.55 Å R-free 0.244
7UZN CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH BMT-206059 AKA 2-{(3M)-3-(1,4-DIMETHYL-1H-1,2,3-TRIAZOL-5-YL)-8-FLUORO-5-[(S)-(OXAN-4-YL)(PHENYL)METHYL]-5H-PYRIDO[3,2-b]INDOL-7-YL}PROPAN-2-OL, TRIPLY DEUTERATED ON THE 4-METHYL GROUP Deposited 2022-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：first bromodomain
Not recorded PQF 2-{(3M)-3-(1,4-dimethyl-1H-1,2,3-triazol-5-yl)-8-fluoro-5-[(S)-(oxan-4-yl)(phenyl)methyl]-5H-pyrido[3,2-b]indol-7-yl}propan-2-ol × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；100 mM bis-tris propane, pH 8.5, 200 mM NaNO3, 20.5%(w/v) PEG 3350
Resolution 1.69 Å R-free 0.217
7V1U Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor ZJ12 Deposited 2021-08-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5E3 ~{N}-(3-ethyl-6-methoxy-1,2-benzoxazol-5-yl)-2-methoxy-benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；30% PEG5000, 0.2M (NH4)2SO4, 0.1M MES monohydrate, PH6.5
Resolution 1.82 Å R-free 0.259
7V2J Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 33 Deposited 2021-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5FZ ~{N}-(3-ethyl-6-methoxy-1,2-benzoxazol-5-yl)-4-methoxy-benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M TRIS HCl, pH 8.5, 8% PEG8000
Resolution 2.24 Å R-free 0.241
7W3D Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N2-(1,2,3-benzotriazol-5-yl)-N3-(dimethylsulfamoyl)-N6-[(2S)-1-methoxypropan-2-yl]pyridine-2,3,6-triamine Deposited 2021-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded 89T N2-(1,2,3-benzotriazol-5-yl)-N3-(dimethylsulfamoyl)-N6-[(2S)-1-methoxypropan-2-yl]pyridine-2,3,6-triamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；287 K；6M sodium formate, 10% glycerol
Resolution 1.98 Å R-free 0.325
7WJS Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13157 Deposited 2022-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded JFL 2-(2-cyclobutyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.73 Å R-free 0.215
7WJS Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13157 Deposited 2022-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded JFL 2-(2-cyclobutyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.73 Å R-free 0.215
7WJS Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13157 Deposited 2022-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded JFL 2-(2-cyclobutyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；1.5 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.73 Å R-free 0.215
7WKY Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded JFR 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.83 Å R-free 0.246
7WKY Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded JFR 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.83 Å R-free 0.246
7WKY Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y13153 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded JFR 2-(2-cyclopentyl-1~{H}-imidazol-5-yl)-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.2 M Potassium sodium tartrate tetrahydrate, 0.1 M BIS-TRIS propane pH 7.0
Resolution 2.83 Å R-free 0.246
7WL4 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor SLP-50 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded JFU ~{N}-[2-ethyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]-2,4-bis(fluoranyl)benzenesulfonamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.82 Å R-free 0.221
7WL4 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor SLP-50 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.82 Å R-free 0.221
7WL4 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor SLP-50 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded JFU ~{N}-[2-ethyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]-2,4-bis(fluoranyl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.82 Å R-free 0.221
7WL4 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor SLP-50 Deposited 2022-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded JFU ~{N}-[2-ethyl-6-(4-methylpiperazin-1-yl)-3-oxidanylidene-2,7-diazatricyclo[6.3.1.0^{4,12}]dodeca-1(12),4,6,8,10-pentaen-9-yl]-2,4-bis(fluoranyl)benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550
Resolution 1.82 Å R-free 0.221
7WWZ BRD4-BD1 complexed with NEO2734 Deposited 2022-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：bromodomain
Not recorded 7OW 1,3-dimethyl-5-[2-(oxan-4-yl)-3-[2-(trifluoromethyloxy)ethyl]benzimidazol-5-yl]pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6；289 K；PEG3350, NaNO3, ethylene glycol
Resolution 1.16 Å R-free 0.191
7X6T Discovery of Selective BRD4 BD1 Inhibitor Based on [1,2,4] triazolo [4,3-b] pyridazine Scaffold Deposited 2022-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–165（124 aa） Fragment：bromodomain 1
Not recorded 97F (2~{R})-2-[[3-methyl-6-(2-phenoxyphenyl)-[1,2,4]triazolo[4,3-b]pyridazin-8-yl]amino]propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.9M~3.9M sodium formate
Resolution 1.44 Å R-free 0.198
7YL2 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor Y07004 Deposited 2022-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded JCO N-(1-ethyl-2-oxidanylidene-3H-indol-5-yl)cyclohexanesulfonamide × 1 GOL GLYCEROL × 1 NO3 NITRATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；0.2M Na2NO3, 0.1M HEPES, 20% PEG3350, 10% EtGhly, PH 7.8
Resolution 1.62 Å R-free 0.204
7YMG Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 2-({3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}amino)-3-(1H-indol-3-yl)propan-1-ol Deposited 2022-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded NA SODIUM ION × 1 JHO (2S)-2-[(3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)amino]-3-(1H-indol-3-yl)propan-1-ol × 1 FMT FORMIC ACID × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；287 K；Protein concentration 12 mg/mL Protein Stoarage buffer: 10mM HEPES pH 7.5, 500mM NaCl, 5% Glycerol, 10 mM DTT Reservoir solution: 5M sodium formate, 6% glycerol (Protein/reservoir= 1000nL/1000nL) co-crystallization: added 5 mM chemical and incubated overnight at 4 celsius.
Resolution 1.40 Å R-free 0.196
7YMG Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 2-({3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl}amino)-3-(1H-indol-3-yl)propan-1-ol Deposited 2022-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1
Not recorded NA SODIUM ION × 1 JHO (2S)-2-[(3-ethyl-[1,2,4]triazolo[4,3-b]pyridazin-6-yl)amino]-3-(1H-indol-3-yl)propan-1-ol × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；287 K；Protein concentration 12 mg/mL Protein Stoarage buffer: 10mM HEPES pH 7.5, 500mM NaCl, 5% Glycerol, 10 mM DTT Reservoir solution: 5M sodium formate, 6% glycerol (Protein/reservoir= 1000nL/1000nL) co-crystallization: added 5 mM chemical and incubated overnight at 4 celsius.
Resolution 1.40 Å R-free 0.196
7YQ9 Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N-[2-(1H-indol-3-yl)ethyl]-3-(trifluoromethyl)[1,2,4]triazolo[4,3-b]pyridazin-6-amine Deposited 2022-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded CL CHLORIDE ION × 1 JLX N-[2-(1H-indol-3-yl)ethyl]-3-(trifluoromethyl)-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；287 K；protein concentration 12 mg/mL Protein storage buffer: 10 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol 10 mM DTT Reservoir solution: 6M sodium formate, 6% glycerol Protein: reservoir solution=1:1 co-crystallization: added 5mM chemical and incubated overnight at 4 celsius
Resolution 1.50 Å R-free 0.201
7YQ9 Crystal structure of BRD4 bromodomain 1 (BD1) in complex with N-[2-(1H-indol-3-yl)ethyl]-3-(trifluoromethyl)[1,2,4]triazolo[4,3-b]pyridazin-6-amine Deposited 2022-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1
Not recorded CL CHLORIDE ION × 1 JLX N-[2-(1H-indol-3-yl)ethyl]-3-(trifluoromethyl)-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；287 K；protein concentration 12 mg/mL Protein storage buffer: 10 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol 10 mM DTT Reservoir solution: 6M sodium formate, 6% glycerol Protein: reservoir solution=1:1 co-crystallization: added 5mM chemical and incubated overnight at 4 celsius
Resolution 1.50 Å R-free 0.201
7ZE6 BRD4 in complex with FragLite10 Deposited 2022-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded GOL GLYCEROL × 1 1P8 6-bromo-1,3-dihydro-2H-indol-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.04 Å R-free 0.233
7ZE7 BRD4 in complex with FragLite21 Deposited 2022-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded UUJ 5-bromo-2-hydroxybenzonitrile × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.23 Å R-free 0.236
7ZEF BRD4 in complex with FragLite22 Deposited 2022-03-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded UUG (4-bromo-2-methoxyphenyl)methanol × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.12 Å R-free 0.233
7ZFN BRD4 in complex with FragLite24 Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded GOL GLYCEROL × 1 IT4 4-bromanyl-2-oxidanyl-benzoic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.12 Å R-free 0.244
7ZFS BRD4 in complex with FragLite32 Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded GOL GLYCEROL × 1 IS0 4-bromanyl-1,2-dimethoxy-benzene × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.25 Å R-free 0.227
7ZFT BRD4 in complex with FragLite33 Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded HWC 3-azanyl-5-bromanyl-1-methyl-pyridin-2-one × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.28 Å R-free 0.252
7ZFU BRD4 in complex with PepLite-Pro Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded IS6 (2R)-N-(3-bromanylprop-2-ynyl)-1-ethanoyl-pyrrolidine-2-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.29 Å R-free 0.204
7ZFV BRD4 in complex with PepLite-Ala Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded GOL GLYCEROL × 1 IJR (2~{S})-2-acetamido-~{N}-(3-bromanylprop-2-ynyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.37 Å R-free 0.223
7ZFY BRD4 in complex with PepLite-Gly Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded ISK 2-acetamido-N-(3-bromanylprop-2-ynyl)ethanamide × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.15 Å R-free 0.213
7ZFZ BRD4 in complex with PepLite-Val Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded GOL GLYCEROL × 2 IT8 (2R)-2-acetamido-N-(3-bromanylprop-2-ynyl)-3-methyl-butanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.08 Å R-free 0.236
7ZG1 BRD4 in complex with PepLite-Tyr Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded T9J Nalpha-acetyl-N-(3-bromoprop-2-yn-1-yl)-L-tyrosinamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.16 Å R-free 0.250
7ZG2 BRD4 in complex with Acetyl-Lys Deposited 2022-04-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded GOL GLYCEROL × 3 8WS (2S)-2,6-diacetamido-N-methyl-hexanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.18 Å R-free 0.231
7ZNT CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 333–460（128 aa）
Not recorded IZR (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% (W/V) PEG 8000, 0.1 M TRIS-HCL (PH REMARK 280 7.5) AND 0.1 M MGCL2,
Resolution 3.00 Å R-free 0.255
7ZNT CRYSTAL STRUCTURE OF AT7 IN COMPLEX WITH THE SECOND BROMODOMAIN OF HUMAN BRD4 AND PVHL:ELONGINC:ELONGINB Deposited 2022-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 333–460（128 aa）
Not recorded IZR (2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；10% (W/V) PEG 8000, 0.1 M TRIS-HCL (PH REMARK 280 7.5) AND 0.1 M MGCL2,
Resolution 3.00 Å R-free 0.255
8B5B Human BRD4 bromdomain 1 in complex with a H4 peptide containing acetyl lysine and ApmTri (H4K5acK8ApmTri) Deposited 2022-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000
Resolution 1.92 Å R-free 0.246
8B5B Human BRD4 bromdomain 1 in complex with a H4 peptide containing acetyl lysine and ApmTri (H4K5acK8ApmTri) Deposited 2022-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000
Resolution 1.92 Å R-free 0.246
8B5B Human BRD4 bromdomain 1 in complex with a H4 peptide containing acetyl lysine and ApmTri (H4K5acK8ApmTri) Deposited 2022-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 44–168（125 aa）
Not recorded PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000
Resolution 1.92 Å R-free 0.246
8B5C Human BRD4 bromdomain 1 in complex with a H4 peptide containing ApmTri (H4K5/8ApmTri) Deposited 2022-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000
Resolution 1.58 Å R-free 0.208
8B96 Crystal structure of the human BRD4-BD1 bromodomain in complex with the inhibitor CRCM5464 Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded Q2F ~{N}-[[4-[[7-ethyl-2,6-bis(oxidanylidene)purin-3-yl]methyl]cyclohexyl]methyl]-3-fluoranyl-4-(oxan-4-yloxy)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.3M NaNO3, 16% PEG3350, 5% Ethylene Glycol
Resolution 1.34 Å R-free 0.195
8B98 Crystal structure of the human BRD4-BD1 bromodomain in complex with the inhibitor CRCM5483 Deposited 2022-10-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded Q2F ~{N}-[[4-[[7-ethyl-2,6-bis(oxidanylidene)purin-3-yl]methyl]cyclohexyl]methyl]-3-fluoranyl-4-(oxan-4-yloxy)benzenesulfonamide × 1 EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.3M NaNO3, 18% PEG3350
Resolution 1.50 Å R-free 0.200
8BDS Ternary complex between VCB, BRD4-BD1 and PROTAC 48 Deposited 2022-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 44–168（125 aa）
Not recorded SO4 SULFATE ION × 4 EDO 1,2-ETHANEDIOL × 6 QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.4M Ammonium Sulfate, 4% (w/v) glycerol, 0.1M HEPES pH 7.5
Resolution 1.72 Å R-free 0.197
8BDT Ternary complex between VCB, BRD4-BD2 and PROTAC 51 Deposited 2022-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 333–460（128 aa）
Not recorded QLX (2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M sodium malonate dibasic monohydrate, 20% (w/v) PEG 3350
Resolution 2.70 Å R-free 0.243
8BDT Ternary complex between VCB, BRD4-BD2 and PROTAC 51 Deposited 2022-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 333–460（128 aa）
Not recorded QLX (2~{S},4~{R})-~{N}-[(1~{S})-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M sodium malonate dibasic monohydrate, 20% (w/v) PEG 3350
Resolution 2.70 Å R-free 0.243
8BDX Ternary complex between VCB, BRD4-BD2 and PROTAC 48 Deposited 2022-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 333–460（128 aa）
Not recorded QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.02M sodium/potassium phosphate, 0.1M bis-Tris propane pH 7.5
Resolution 2.93 Å R-free 0.258
8BDX Ternary complex between VCB, BRD4-BD2 and PROTAC 48 Deposited 2022-10-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 333–460（128 aa）
Not recorded QIY (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；20% PEG 3350, 0.02M sodium/potassium phosphate, 0.1M bis-Tris propane pH 7.5
Resolution 2.93 Å R-free 0.258
8BEB Ternary complex between VCB, BRD4-BD1 and PROTAC 49 Deposited 2022-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 44–168（125 aa）
Not recorded SO4 SULFATE ION × 1 QIK (2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]butylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.8M ammonium sulfate, 4% (w/v) glycerol, 0.1M bis-Tris pH5.5
Resolution 3.18 Å R-free 0.274
8C11 BRD4 in complex with 2-(2-(4-(3,5-dimethylisoxazol-4-yl)-1H-pyrazol-1-yl)acetamido)-N-ethylpropanamide Deposited 2022-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded SY0 (2~{S})-2-[2-[4-(3,5-dimethyl-1,2-oxazol-4-yl)pyrazol-1-yl]ethanoylamino]-~{N}-ethyl-propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution
Resolution 1.80 Å R-free 0.234
8CKF Crystal Structure of the first bromodomain of human BRD4 L94C variant in complex with racemic 3,5-dimethylisoxazol ligand Deposited 2023-02-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：L94C E5Q 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(~{R})-oxidanyl(pyridin-3-yl)methyl]phenol × 1 V0R 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(~{S})-oxidanyl(pyridin-3-yl)methyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.15 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Resolution 1.88 Å R-free 0.260
8DYR BRD4-D1 in complex with BET inhibitor Deposited 2022-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded U59 (4P,6P)-4-[2-(cyclopropylmethoxy)-5-(methanesulfonyl)phenyl]-6-[1-(2-fluoroethyl)-1H-1,2,3-triazol-4-yl]-2-methylisoquinolin-1(2H)-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200 mM Magnesium Chloride, 100 mM HEPES pH 7.5, 25% PEG 3350
Resolution 1.47 Å R-free 0.197
8E17 BRD4-D1 in complex with BET inhibitor Deposited 2022-08-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded U7R (4P,6M)-6-[1-(2-fluoroethyl)-1H-1,2,3-triazol-4-yl]-4-[5-(methanesulfonyl)-2-methoxyphenyl]-2-methylisoquinolin-1(2H)-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；170 mM Sodium Acetate, 85 mM TRIS pH 8.5, 25% PEG 4000
Resolution 1.47 Å R-free 0.184
8E3W BRD4-D1 in complex with BET inhibitor Deposited 2022-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded UHI (4P)-4-[2-(cyclopropylmethoxy)-5-(methanesulfonyl)phenyl]-2-methylisoquinolin-1(2H)-one × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；24.1% PEG 3350, 200 mM KCl
Resolution 1.47 Å R-free 0.192
8EAD Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with dual BRD4-JAK2 inhibitor MA9-177 Deposited 2022-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 UY0 N-{2-chloro-5-[(5-methyl-2-{4-[2-(pyrrolidin-1-yl)ethoxy]anilino}pyrimidin-4-yl)amino]phenyl}-2-methylpropane-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium sulphate, 0.15 M Sodium chloride, 0.1 M Tris (pH 8.5), 25 % w/v PEG 3,350
Resolution 1.65 Å R-free 0.195
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain L 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain T 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8EWV DNA-encoded library (DEL)-enabled discovery of proximity inducing small molecules Deposited 2022-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain X 44–168（125 aa）
Not recorded X5K N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；0.2 M NA2MALON, 20 %W/V PEG 3350
Resolution 3.40 Å R-free 0.324
8FVK First bromodomain of BRD4 liganded with CCS-1477 Deposited 2023-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：bromodomain 1
Not recorded JHL (6S)-1-[3,4-bis(fluoranyl)phenyl]-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]piperidin-2-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M Ammonium sulfate, 0.1M Tris pH8.5, 25% w/v Polyethylene glycol 3350
Resolution 1.53 Å R-free 0.189
8FVK First bromodomain of BRD4 liganded with CCS-1477 Deposited 2023-01-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1
Not recorded JHL (6S)-1-[3,4-bis(fluoranyl)phenyl]-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(4-methoxycyclohexyl)benzimidazol-2-yl]piperidin-2-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2M Ammonium sulfate, 0.1M Tris pH8.5, 25% w/v Polyethylene glycol 3350
Resolution 1.53 Å R-free 0.189
8G46 Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Deposited 2023-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 333–460（128 aa）
Not recorded ZN ZINC ION × 1 YK3 tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP, 0.011% LMNG
cryo-EM vitrification conditions Cryogen ETHANE；detergent added directly before grid application
Resolution 2.20 Å
8GPZ Crystal structure of BRD4 bromodomain 1 (BD1) in complex with C239-0012 Deposited 2022-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded FMT FORMIC ACID × 2 NA SODIUM ION × 1 KC3 3-methyl-6-(4-methylpiperidin-1-yl)-[1,2,4]triazolo[4,3-b]pyridazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；6 M Sodium formate, 10% Glycerol
Resolution 1.53 Å R-free 0.212
8GQ0 Crystal structure of BRD4 bromodomain 1 (BD1) in complex with STL233497 Deposited 2022-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa）
Not recorded FMT FORMIC ACID × 4 NA SODIUM ION × 2 GOL GLYCEROL × 2 KCL ~{N}-[2-(1~{H}-indol-3-yl)ethyl]-3-methyl-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；6 M Sodium formate, 10% Glycerol
Resolution 1.44 Å R-free 0.189
8IBQ Bromodomain and Extra-terminal Domain (BET) BRD4 Deposited 2023-02-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–165（122 aa）
Not recorded OWO 7-[2-fluoranyl-3-(1,3,5-trimethylpyrazol-4-yl)phenyl]-1~{H}-imidazo[4,5-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；3.6M Naformate 10% glycerol
Resolution 1.45 Å R-free 0.244
8IDH Bromodomain and Extra-terminal Domain (BET) BRD4 Deposited 2023-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 349–460（112 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) OWO 7-[2-fluoranyl-3-(1,3,5-trimethylpyrazol-4-yl)phenyl]-1~{H}-imidazo[4,5-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；0.2M NaCl,0.1M bistris,18-28%PEG3350
Resolution 1.57 Å R-free 0.252
8K14 X-ray crystal structure of 18a in BRD4(1) Deposited 2023-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded VFI 4-[8-methoxy-2-methyl-1-(1-phenylethyl)imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 2.0 M Ammonium sulfate
Resolution 1.28 Å R-free 0.174
8OV6 Ternary structure of intramolecular bivalent glue degrader IBG1 bound to BRD4 and DCAF16:DDB1deltaBPB Deposited 2023-04-25 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 42–459（418 aa）
Not recorded ZN ZINC ION × 1 U79 methyl 2-[(9~{S})-7-[4-[4-[[4-[(3-cyano-4-methyl-1~{H}-indol-7-yl)sulfamoyl]phenyl]methylcarbamoyl]phenyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；3.5 uL complex was dispensed onto the grid, allowed to disperse for 10 s, blotted for 3.5 s using blot force 3, then plunged into liquid ethane
Resolution 3.77 Å
8P9F Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB161 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded X9O ~{N}-(2-aminophenyl)-4-[2-(2-azanyl-5-methyl-4-oxidanyl-phenyl)hydrazinyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB161. Crystallization buffer: 25% PEG 3350, 0.15 M Na nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.6. Vol ratio 1:1
Resolution 1.30 Å R-free 0.215
8P9G Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB390 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded X9K ~{N}-(2-aminophenyl)-4-[(~{E})-(6-methyl-7-oxidanyl-1~{H}-indol-4-yl)diazenyl]benzamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB390. Crystallization buffer: 25% PEG 3350, 0.2 M Na formate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.9. Vol. ratio 1:1
Resolution 1.10 Å R-free 0.183
8P9H Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB437 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded X9C ~{N}-(2-aminophenyl)-2-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)quinoline-6-carboxamide × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB437. Reservoir buffer: 25% PEG 3350, 0.2 M Na nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.9. Vol. ratio 1:2
Resolution 1.19 Å R-free 0.173
8P9I Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB462 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded X8T ~{N}-(2-aminophenyl)-4-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB462. Crystallization buffer: 24% PEG 3350, 0.15 M Na formate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.6. Vol. ratio 1:2
Resolution 1.23 Å R-free 0.193
8P9I Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB462 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded X8T ~{N}-(2-aminophenyl)-4-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB462. Crystallization buffer: 24% PEG 3350, 0.15 M Na formate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.6. Vol. ratio 1:2
Resolution 1.23 Å R-free 0.193
8P9J Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB500 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded X8O ~{N}-(2-aminophenyl)-5-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)pyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB500. Crystallization buffer: 25% PEG 3350, 0.1 M Na nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.3. Vol ratio 1:1
Resolution 1.42 Å R-free 0.206
8P9K Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB503 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 X9U ~{N}-(2-azanyl-5-phenyl-phenyl)-4-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB503. Crystallization buffer: 25% PEG 3350, 0.1 M Na malonate pH 7, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.3. Vol ratio 1:2
Resolution 1.25 Å R-free 0.175
8P9L Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB512 Deposited 2023-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded XA3 ~{N}-(2-azanyl-5-phenyl-phenyl)-5-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)pyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM inhibitor NB512. Reservoir buffer: 24% PEG 3350, 0.1 M Na/K Tartrate, 10% ethylene glycol, 0.1 M bis-tris propane pH 7.3. Vol ratio 1:2
Resolution 1.29 Å R-free 0.188
8PIQ Crystal Structure of BRD4-BD1 with BI894999 Deposited 2023-06-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZHO ~{N},3-dimethyl-6-[6-(4-methylpiperazin-1-yl)-1-(phenylmethyl)benzimidazol-2-yl]-[1,2,4]triazolo[4,3-a]pyrazin-8-amine × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100mM Imidazole pH 6.9 13.5% w/v PEG8000
Resolution 1.12 Å R-free 0.187
8PXA N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (S)-5-(1-((1-(1-isopropylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one Deposited 2023-07-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–168（125 aa）
Not recorded I0Z 1,3-dimethyl-5-[1-[[(3~{S})-1-(1-propan-2-ylpiperidin-4-yl)carbonylpiperidin-3-yl]methyl]benzimidazol-2-yl]pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 12% w/v PEG4K
Resolution 1.30 Å R-free 0.217
8PXM N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(pentane-1,5-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded ZTY (1R)-7-[5-[[(1R)-1,3-dimethyl-2-oxidanylidene-1H-3-benzazepin-7-yl]oxy]pentoxy]-1,3-dimethyl-1H-3-benzazepin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 0.2M lithium sulphate, 16% w/v PEG4K
Resolution 2.38 Å R-free 0.309
8PXM N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(pentane-1,5-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 0.2M lithium sulphate, 16% w/v PEG4K
Resolution 2.38 Å R-free 0.309
8PXN N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(ethane-1,2-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ZTT (1R)-7-[2-[[(1R)-1,3-dimethyl-2-oxidanylidene-1H-3-benzazepin-7-yl]oxy]ethoxy]-1,3-dimethyl-1H-3-benzazepin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 12% w/v 4K
Resolution 1.95 Å R-free 0.270
8PXN N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(ethane-1,2-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 12% w/v 4K
Resolution 1.95 Å R-free 0.270
8PXN N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(ethane-1,2-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 12% w/v 4K
Resolution 1.95 Å R-free 0.270
8PXN N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(ethane-1,2-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one) Deposited 2023-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 ZTT (1R)-7-[2-[[(1R)-1,3-dimethyl-2-oxidanylidene-1H-3-benzazepin-7-yl]oxy]ethoxy]-1,3-dimethyl-1H-3-benzazepin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1M Tris pH8.5, 12% w/v 4K
Resolution 1.95 Å R-free 0.270
8Q34 Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a Deposited 2023-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–171（128 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 IX4 ~{N}-(1~{H}-imidazo[4,5-b]pyridin-2-ylmethyl)-3-(3-methyl-1,2-diazirin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride
Resolution 1.48 Å R-free 0.216
8Q34 Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a Deposited 2023-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–171（128 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 IX4 ~{N}-(1~{H}-imidazo[4,5-b]pyridin-2-ylmethyl)-3-(3-methyl-1,2-diazirin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride
Resolution 1.48 Å R-free 0.216
8Q34 Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a Deposited 2023-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–171（128 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 IX4 ~{N}-(1~{H}-imidazo[4,5-b]pyridin-2-ylmethyl)-3-(3-methyl-1,2-diazirin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride
Resolution 1.48 Å R-free 0.216
8Q34 Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a Deposited 2023-08-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–171（128 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 IX4 ~{N}-(1~{H}-imidazo[4,5-b]pyridin-2-ylmethyl)-3-(3-methyl-1,2-diazirin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride
Resolution 1.48 Å R-free 0.216
8QAL Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 83 Deposited 2023-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：First bromodomain (residues 1796-1899) GQX 2-[4-(3-methyl-4-oxidanylidene-2,5,6,7-tetrahydroisoindol-1-yl)-1,3-thiazol-2-yl]guanidine × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol
Resolution 1.30 Å R-free 0.171
8QAN Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 79 Deposited 2023-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：First bromodomain (residues 1796-1899) GKI 1-[2-methyl-4-(3-methylbutyl)-5-(2-piperazin-1-yl-1,3-thiazol-4-yl)-1~{H}-pyrrol-3-yl]ethanone × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol
Resolution 1.25 Å R-free 0.176
8QAP Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 2 Deposited 2023-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：First bromodomain (residues 1796-1899) Q9U 2-[4-(3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-2~{H}-isoindol-1-yl)-1,3-thiazol-2-yl]guanidine × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol
Resolution 1.40 Å R-free 0.186
8QAR Crystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 98 Deposited 2023-08-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Mutation：First bromodomain (residues 1796-1899) GI0 3-methyl-1-[2-[4-[(4-methyl-1~{H}-pyrazol-3-yl)methyl]piperazin-1-yl]-1,3-thiazol-4-yl]-2,5,6,7-tetrahydroisoindol-4-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；16% PEG 3350, 20% ethylene glycol
Resolution 1.50 Å R-free 0.201
8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 346–460（115 aa）
Mutation：C356A C357A K368C C391A C429A ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.44 Å
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 333–460（128 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 333–460（128 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RWZ Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL Deposited 2024-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 347–460（114 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 349–459（111 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8V92 BRD4 BD1 liganded with macrocyclic compound 2b (JJ-II-352A) Deposited 2023-12-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1AAL (4bS)-1-ethyl-21-methyl-4b,11,12,22-tetrahydro-2H,10H,18H-dibenzo[13',14':6',7'][1,5,9]trioxacyclotetradecino[12',11':4,5]pyrido[2,3-d]pyrimidine-2,4,20(1H,3H)-trione × 1 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；50 mM Tris pH 8.5, 0.1 M ammonium sulfate, 12.5% PEG 3,350
Resolution 1.27 Å R-free 0.158
8V9F BRD4 BD1 liganded with macrocyclic compound 2d (JJ-II-363A) Deposited 2023-12-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded YPB (4bS)-1-ethyl-7,20-dimethyl-4b,10,11,21-tetrahydro-2H,17H-dibenzo[12',13':5',6'][1,4,8]trioxacyclotridecino[11',10':4,5]pyrido[2,3-d]pyrimidine-2,4,19(1H,3H)-trione × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Resolution 1.22 Å R-free 0.200
8WIU Bromodomain and Extra-terminal Domain (BET) BRD4 Deposited 2023-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–165（124 aa） Fragment：bromodomain 1
Not recorded WPR 7-[5-[1-(cyclopropylmethyl)-3,5-dimethyl-pyrazol-4-yl]pyridin-3-yl]-1~{H}-imidazo[4,5-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 18-28% w/v Polyethylene glycol 3,350
Resolution 1.40 Å R-free 0.236
8WQO Crystal structure of BRD4-BD1 bound with DI106 Deposited 2023-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–165（124 aa） Fragment：bromodomain 1
Not recorded X3L (3~{R})-6-[[4-(3,5-dimethyl-1~{H}-pyrazol-4-yl)pyrimidin-2-yl]amino]-1,3-dimethyl-4-propan-2-yl-3~{H}-quinoxalin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.4 M sodium formate and 10 % glycerol
Resolution 1.13 Å R-free 0.212
8WXY Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 23 Deposited 2023-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Chain C 44–168（125 aa）
Not recorded XGN 5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-4-[(2-morpholin-4-yl-2-oxidanylidene-ethyl)amino]pyridin-2-one × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.9；277 K；1.8 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 6.9
Resolution 2.87 Å R-free 0.249
8WY3 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 21 Deposited 2023-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Chain C 44–168（125 aa）
Not recorded XHE ~{N}-cyclopropyl-2-[[5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-2-oxidanylidene-pyridin-4-yl]amino]ethanamide × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；2.0 M Sodium formate, 0.1 M Tris pH 8.5
Resolution 2.78 Å R-free 0.234
8WY7 Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 22 Deposited 2023-10-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 44–168（125 aa）
Chain B 44–168（125 aa）
Chain C 44–168（125 aa）
Not recorded XHN 2-[[5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-2-oxidanylidene-pyridin-4-yl]amino]-~{N}-(4-oxidanylcyclohexyl)ethanamide × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；2.0 M Sodium formate, 0.1 M Tris pH 8.5
Resolution 2.83 Å R-free 0.281
8WYP High Resolution Crystal Structure of Brd4 BD-1 in Complex with a Novel Inhibitor Precursor Deposited 2023-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–167（124 aa）
Not recorded XUK 3-bromanylimidazo[1,2-a]pyridin-6-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；4.0 M sodium formate and 200 mM NDSB-201
Resolution 1.24 Å R-free 0.214
8X7G Crystal structure of the ternary complex of GID4-PROTAC(NEP108)-BRD4(BD1). Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded YAX 2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]-~{N}-[2-[2-[[2-[4-[2-(1~{H}-indol-2-ylmethylamino)ethanoylamino]cyclohexyl]-3~{H}-benzimidazol-5-yl]oxy]ethoxy]ethyl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Bis-Tris pH 6.5, 25% (v/v) polyethylene glycol 300, 30% (v/v) galactose
Resolution 2.70 Å R-free 0.266
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 44–168（125 aa）
Not recorded YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 44–168（125 aa）
Not recorded YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
Resolution 2.90 Å R-free 0.301
8X7H Crystal structure of the ternary complex of GID4-PROTAC(NEP162)-BRD4(BD1). Deposited 2023-11-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 44–168（125 aa）
Not recorded YBI ~{N}-[4-[6-[3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoyl]piperazin-1-yl]propoxy]-1~{H}-benzimidazol-2-yl]cyclohexyl]-2-(1~{H}-indol-2-ylmethylamino)ethanamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris pH 6.5, 10% (w/v) polyethylene glycol 10000
Resolution 2.90 Å R-free 0.301
8YMB The crystal structure of SHD931 in complex with Brd4-BD2 and VCB Deposited 2024-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 333–460（128 aa）
Not recorded CL CHLORIDE ION × 5 A1LY0 SHD931 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1500 mM Ammonium sulfate, 100 mM Tris base/ Hydrochloric acid, pH 8.5, 12% (v/v) Glycerol
Resolution 2.95 Å R-free 0.270
8YMB The crystal structure of SHD931 in complex with Brd4-BD2 and VCB Deposited 2024-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 333–460（128 aa）
Not recorded CL CHLORIDE ION × 3 A1LY0 SHD931 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；1500 mM Ammonium sulfate, 100 mM Tris base/ Hydrochloric acid, pH 8.5, 12% (v/v) Glycerol
Resolution 2.95 Å R-free 0.270
8YME BRD4-BD1 in complex with N-cyclohexyl-1-methyl-6-{[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxo-pyrazolo[4,3-c]pyridin-2-yl]methyl}azepan-1-ium-4-carboxamide 2,2,2-trifluoroacetate Deposited 2024-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1LZZ (4R,6S)-N-cyclohexyl-1-methyl-6-[[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxidanylidene-pyrazolo[4,3-c]pyridin-2-yl]methyl]azepane-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Resolution 1.18 Å R-free 0.186
8YMF BRD4-BD1 in complex with 7-[2-(cyclopropylmethoxy)phenyl]-5-methyl-2-[(1-methylsulfonyl-4-piperidyl)methyl]pyrazolo[4,3-c]pyridin-4-one Deposited 2024-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1LZB 7-[2-(cyclopropylmethoxy)phenyl]-5-methyl-2-[(1-methylsulfonylpiperidin-4-yl)methyl]pyrazolo[4,3-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Resolution 1.01 Å R-free 0.171
8YMG BRD4-BD1 in complex with 7-[4-chloro-1-(tetrahydropyran-4-ylmethyl)imidazol-2-yl]-5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}furo[3,2-c]pyridin-4-one Deposited 2024-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1LZC 7-[4-chloro-1-(tetrahydropyran-4-ylmethyl)imidazol-2-yl]-5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}furo[3,2-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Resolution 1.01 Å R-free 0.162
8YMH BRD4-BD1 in complex with 5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}-7-(1-methylpyrazol-3-yl)furo[3,2-c]pyridin-4-one Deposited 2024-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1LZE 5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}-7-(1-methylpyrazol-3-yl)furo[3,2-c]pyridin-4-one × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Resolution 1.04 Å R-free 0.208
8YMI BRD4-BD1 in complex with 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)pyrazolo[4,3-c]pyridin-4-one Deposited 2024-03-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1LZF 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)pyrazolo[4,3-c]pyridin-4-one × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Resolution 1.01 Å R-free 0.211
8ZM8 Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13221 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1L1X 2-[2-ethyl-4-(methoxymethyl)-1~{H}-imidazol-5-yl]-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.0 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 8.2
Resolution 3.00 Å R-free 0.265
8ZM8 Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13221 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded A1L1X 2-[2-ethyl-4-(methoxymethyl)-1~{H}-imidazol-5-yl]-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.0 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 8.2
Resolution 3.00 Å R-free 0.265
8ZM8 Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13221 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded A1L1X 2-[2-ethyl-4-(methoxymethyl)-1~{H}-imidazol-5-yl]-7-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-5-methyl-furo[3,2-c]pyridin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.0 M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic / pH 8.2
Resolution 3.00 Å R-free 0.265
8ZMB Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13195 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1L0Y 7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Resolution 2.79 Å R-free 0.244
8ZMB Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13195 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded A1L0Y 7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Resolution 2.79 Å R-free 0.244
8ZMB Crystal Structure of the first bromodomain of human BRD4 BD1 in complex with the inhibitor Y13195 Deposited 2024-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded A1L0Y 7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate
Resolution 2.79 Å R-free 0.244
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 10 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 11 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain K 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 12 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 13 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain M 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 14 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain N 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 15 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain O 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 16 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain P 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 17 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain Q 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 18 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain R 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 19 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain S 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 20 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain T 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
8ZMQ Crystal Structure of the second bromodomain of human BRD4 BD2 in complex with the inhibitor Y13190 Deposited 2024-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 333–460（128 aa）
Not recorded A1L12 2-(2-(adamantan-1-yl)-4-ethyl-1H-imidazol-5-yl)-7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methylfuro[3,2-c]pyridin-4(5H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.01 M Iron(III) chloride hexahydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 10% v/v Jeffamine M-600
Resolution 2.20 Å R-free 0.274
9C5V Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex Deposited 2024-06-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 49–170（122 aa）
Not recorded A1AUO N-({4-[(4-{[1'-(chloroacetyl)-3'-oxo-3',4'-dihydro-1'H-spiro[cyclopentane-1,2'-quinoxalin]-6'-yl]oxy}piperidin-1-yl)methyl]phenyl}methyl)-2-[(6S,10P)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9F1J First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 14 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 A1H84 N-[2-[2-[2-[2-[2-[2-[2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]-4-[4-[2-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-(2-morpholin-4-ylethyl)benzimidazol-2-yl]ethyl]phenoxy]butanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM degrader 14. Crystallization condition: 25% PEG 3350, 0.25 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.2.
Resolution 1.13 Å R-free 0.185
9F1K First bromodomain of BRD4 in complex with ISOX-DUAL based inhibitor 30 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded A1H81 2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]-N-(2-methoxyethyl)ethanamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM inhibitor 30. Crystallization condition: 25% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.61 Å R-free 0.215
9F1L First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 35 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 A1H83 N-[2-[2-[(3R)-2,6-bis(oxidanylidene)piperidin-3-yl]-1,3-bis(oxidanylidene)isoindol-4-yl]oxyethyl]-2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 1 mM degrader 35. Crystallization condition: 25% PEG 3350, 0.2 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 7.9.
Resolution 1.30 Å R-free 0.182
9F1M First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 A1H80 1-[2-[7-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]heptanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 45 Crystallization condition: 24% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.90 Å R-free 0.237
9F1M First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 A1H80 1-[2-[7-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]heptanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 45 Crystallization condition: 24% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.90 Å R-free 0.237
9F1M First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1 A1H80 1-[2-[7-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]heptanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 45 Crystallization condition: 24% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.90 Å R-free 0.237
9F1M First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 45 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1 A1H80 1-[2-[7-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]heptanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 45 Crystallization condition: 24% PEG 3350, 0.3 M sodium nitrate, 15% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.90 Å R-free 0.237
9F1N First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 46 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 3 A1H9H (2S,4R)-1-[(2S)-2-[9-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]nonanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-4H-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 46 Crystallization condition: 25% PEG 3350, 0.3 M sodium malonate pH 7, 10% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.71 Å R-free 0.232
9F1N First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 46 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1H9H (2S,4R)-1-[(2S)-2-[9-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]nonanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-4H-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 46 Crystallization condition: 25% PEG 3350, 0.3 M sodium malonate pH 7, 10% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.71 Å R-free 0.232
9F1N First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 46 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 44–168（125 aa）
Not recorded NA SODIUM ION × 1 A1H9H (2S,4R)-1-[(2S)-2-[9-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]nonanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-4H-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 46 Crystallization condition: 25% PEG 3350, 0.3 M sodium malonate pH 7, 10% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.71 Å R-free 0.232
9F1N First bromodomain of BRD4 in complex with ISOX-DUAL based degrader 46 Deposited 2024-04-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1H9H (2S,4R)-1-[(2S)-2-[9-[2-[4-[2-[2-[2-[4-[3-(dimethylamino)propoxy]phenyl]ethyl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzimidazol-1-yl]ethyl]piperazin-1-yl]ethanoylamino]nonanoylamino]-3,3-dimethyl-butanoyl]-N-[[4-(4-methyl-4H-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution:10 mg/mL in 25 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM TCEP, 5% glycerol, 2 mM degrader 46 Crystallization condition: 25% PEG 3350, 0.3 M sodium malonate pH 7, 10% ethylene glycol, 0.1 M bis-tris propane pH 8.5.
Resolution 1.71 Å R-free 0.232
9FBY N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with (5-(4-chloro-1-((tetrahydro-2H-pyran-4-yl)methyl)-1H-imidazol-2-yl)-1,3-dimethylpyridin-2(1H)-one Deposited 2024-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1IB5 5-[4-chloranyl-1-(oxan-4-ylmethyl)imidazol-2-yl]-1,3-dimethyl-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M MMT(Malic acid, MES, Tris) pH9.0,25% w/v PEG1500
Resolution 1.85 Å R-free 0.219
9FWX Crystal structure of BRD4 BD1 with MEN1404BS. Deposited 2024-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1IGX 3-methyl-~{N}-(2-phenylethyl)-[1,2,4]triazolo[4,3-b]pyridazin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；16.5 % PEG 3350, 0.1 M sodium nitrate, 8 % ethylene glycol
Resolution 1.25 Å R-free 0.190
9FXP Crystal structure of BRD4 BD1 with DI00626383. Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded 5WX 4-methoxy-1,2-benzoxazol-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16.5 % PEG 3350, 0.1 M sodium nitrate, 8 % ethylene glycol
Resolution 1.88 Å R-free 0.218
9HT0 A novel bottom-up approach to find lead-compounds in billion-sized libraries Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1IXD ~{N}-methyl-4-[5-(2-methyl-1-oxidanylidene-isoquinolin-4-yl)-3-(pyrazol-1-ylmethyl)-1,2,4-triazol-1-yl]benzamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292.15 K；Morpheus 0.09M Halogens, 0.1M Buffer System 2 pH6.5, 50% v/v Precipitant Mix 2
Resolution 1.33 Å R-free 0.208
9HT1 A novel bottom-up approach to find lead-compounds in billion-sized libraries Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283.15 K；Morpheus 0.1 Amino acids, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant Mix 1
Resolution 1.94 Å R-free 0.222
9HT1 A novel bottom-up approach to find lead-compounds in billion-sized libraries Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa）
Not recorded A1IXE 1-(2,8-dioxa-5-azaspiro[3.6]decan-5-yl)-2-[[5-methyl-4-(4-methylphenyl)-1,2,4-triazol-3-yl]sulfanyl]ethanone × 1 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；283.15 K；Morpheus 0.1 Amino acids, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant Mix 1
Resolution 1.94 Å R-free 0.222
9HT2 A novel bottom-up approach to find lead-compounds in billion-sized libraries Deposited 2024-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded A1IXF methyl 2,2,6,6-tetramethyl-4-[[2-[(5-methyl-1,3,4-thiadiazol-2-yl)amino]-2-oxidanylidene-ethyl]amino]oxane-4-carboxylate × 1 P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；283.15 K；Morpheus 0.09 M Halogens, 0.1M Buffer system 3 pH 8.5 50% v/v precipitant mix 1
Resolution 1.42 Å R-free 0.186
9IV5 BRD4 in complex with compound7 Deposited 2024-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 42–168（127 aa）
Not recorded A1D95 7-[2-fluoranyl-5-(oxetan-3-ylmethoxy)-3-(1,3,5-trimethylpyrazol-4-yl)phenyl]-1~{H}-imidazo[4,5-b]pyridine × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；6 M sodium formate and 10 % glycerol
Resolution 1.59 Å R-free 0.247
9KEM Crystal structure of BRD4-BD1 in complex with H2AK5acK9ac Deposited 2024-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 54–168（115 aa）
Chain B 54–168（115 aa）
Chain C 54–168（115 aa）
Chain D 54–168（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.94 Å R-free 0.252
9KT2 The crystal structure of BD1 in complex with BDS4 Deposited 2024-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；0.15 M potassium bromide, 30% (v/v) PEG2000MME
Resolution 1.46 Å R-free 0.195
9MPD BRD4-BD1 in complex with cyclic peptide 4.1B Deposited 2024-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 347–464（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.01 M Zinc chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.50 Å R-free 0.270
9MPD BRD4-BD1 in complex with cyclic peptide 4.1B Deposited 2024-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 347–464（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.01 M Zinc chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000
Resolution 2.50 Å R-free 0.270
9MPI BRD4-BD1 in complex with cyclic peptide 4.1A Deposited 2024-12-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；291 K；0.2 M Sodium formate, 20 % w/v PEG 3350
Resolution 2.87 Å R-free 0.325
9MXK BRD4-BD1 in complex with cyclic peptide 4.1C Deposited 2025-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 42% v/v Polyethylene glycol 200
Resolution 1.73 Å R-free 0.213
9MXK BRD4-BD1 in complex with cyclic peptide 4.1C Deposited 2025-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 42–168（127 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 42% v/v Polyethylene glycol 200
Resolution 1.73 Å R-free 0.213
9MXK BRD4-BD1 in complex with cyclic peptide 4.1C Deposited 2025-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 42–168（127 aa）
Not recorded 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 42% v/v Polyethylene glycol 200
Resolution 1.73 Å R-free 0.213
9NN5 BET BRD4-BD1 in complex with peptide 9.2 Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium chloride, 20% w/v Polyethylene glycol 3,350
Resolution 1.47 Å R-free 0.193
9NNT BET BRD4-BD1 in complex with peptide 6.1 Deposited 2025-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris 8.0 Polyethylene glycol 400
Resolution 1.59 Å R-free 0.217
9NNT BET BRD4-BD1 in complex with peptide 6.1 Deposited 2025-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris 8.0 Polyethylene glycol 400
Resolution 1.59 Å R-free 0.217
9NNT BET BRD4-BD1 in complex with peptide 6.1 Deposited 2025-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 42–168（127 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris 8.0 Polyethylene glycol 400
Resolution 1.59 Å R-free 0.217
9QNV CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound 2 Deposited 2025-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 A1I76 3-methyl-5-phenyl-[1,3]thiazolo[2,3-c][1,2,4]triazole × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Resolution 1.23 Å R-free 0.148
9QOB CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound 4 Deposited 2025-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 43–168（126 aa） Fragment：First bromodomain, UNP residues 44-168
Not recorded EDO 1,2-ETHANEDIOL × 2 A1I8D (5-phenyl-[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl)methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Resolution 1.37 Å R-free 0.196
9QW8 FKBP12 in complex with bifunctional ligand 1ad and the first bromodomain of BRD4 Deposited 2025-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded A1JAZ ~{N}-[2-[2-[4-[[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-2-oxidanylidene-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-5-yl]methoxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethyl]-2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG3350, 0.2 M NaCl, 0.1 M Tris-HCl pH 8.5
Resolution 1.80 Å R-free 0.243
9QW8 FKBP12 in complex with bifunctional ligand 1ad and the first bromodomain of BRD4 Deposited 2025-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded A1JAZ ~{N}-[2-[2-[4-[[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-2-oxidanylidene-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-5-yl]methoxymethyl]-1,2,3-triazol-1-yl]ethoxy]ethyl]-2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；22% PEG3350, 0.2 M NaCl, 0.1 M Tris-HCl pH 8.5
Resolution 1.80 Å R-free 0.243
9R5N FKBP12 in complex with binfunctional ligand b3c and the first bromodomain of BRD4 Deposited 2025-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–168（125 aa）
Not recorded A1JCU ~{tert}-butyl 2-[(9~{S})-7-[4-[3-[2-[2-[4-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-2-oxidanylidene-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-5-yl]-1,2,3-triazol-1-yl]ethoxy]ethanoylamino]prop-1-ynyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.2M ammonium thiocyanate, 0.1 M Tris-HCl pH 8.8
Resolution 3.00 Å R-free 0.312
9R5N FKBP12 in complex with binfunctional ligand b3c and the first bromodomain of BRD4 Deposited 2025-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 44–168（125 aa）
Not recorded A1JCU ~{tert}-butyl 2-[(9~{S})-7-[4-[3-[2-[2-[4-[(1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-2-oxidanylidene-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-5-yl]-1,2,3-triazol-1-yl]ethoxy]ethanoylamino]prop-1-ynyl]phenyl]-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.2M ammonium thiocyanate, 0.1 M Tris-HCl pH 8.8
Resolution 3.00 Å R-free 0.312
9RSC Ternary complex of an improved charged molecular glue degrader ZZ2-SO2H, BRD4(BD1) neosubstrate, and the CTLH E3 ligase receptor module YPEL5-WDR26 Deposited 2025-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 44–168（125 aa）
Not recorded ZN ZINC ION × 3 A1IL8 2,6-bis(chloranyl)-4-[[4-[(9S)-4,5,13-trimethyl-9-[2-[(2-methylpropan-2-yl)oxy]-2-oxidanylidene-ethyl]-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-7-yl]phenyl]carbamoyl]benzenesulfinic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.42 Å
9RSD Ternary complex of a charged molecular glue degrader ZZ1-SO2H, BRD4(BD1) neosubstrate, and the CTLH E3 ligase receptor module YPEL5-WDR26 Deposited 2025-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 44–168（125 aa）
Not recorded ZN ZINC ION × 3 A1IL9 2-chloranyl-4-[[4-[(9S)-4,5,13-trimethyl-9-[2-[(2-methylpropan-2-yl)oxy]-2-oxidanylidene-ethyl]-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-7-yl]phenyl]carbamoyl]benzenesulfinic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.38 Å
9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 44–168（125 aa）
Not recorded ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 44–168（125 aa）
Not recorded ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9VCZ The crystal structure of BRD4-BD1 in complex with inhibitor 39b Deposited 2025-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–168（125 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.50 Å R-free 0.197
9VQ1 NMR solution structures of BRD4 ET domain in complex with ASXL1 peptide Deposited 2025-07-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 601–683（83 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 137 mM sodium chloride, 10 mM sodium phosphate, 2 mM DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 137 mM sodium chloride, 10 mM sodium phosphate, 2 mM DTT, 100% D2O | 100% D2O
Resolution not provided
9ZG4 5jc21/CG13250 bound to BRD4-BD1. Deposited 2025-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 44–166（123 aa） Fragment：residues 44-166
Not recorded A1C14 (4P)-4-[4-(benzylamino)-2-oxo-1,2-dihydroquinolin-6-yl]-3,5-dimethyl-2H-1,2-oxazol-1-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；100 mM Magnesium Formate and 15% PEG 3350.
Resolution 1.48 Å R-free 0.228
9ZG4 5jc21/CG13250 bound to BRD4-BD1. Deposited 2025-12-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 44–168（125 aa） Fragment：bromodomain 1
Not recorded A1C14 (4P)-4-[4-(benzylamino)-2-oxo-1,2-dihydroquinolin-6-yl]-3,5-dimethyl-2H-1,2-oxazol-1-ium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；100 mM Magnesium Formate and 15% PEG 3350.
Resolution 1.48 Å R-free 0.228
9ZYT Crystal Structure of BRD4 Bromodomain BD1 in Complex with Small Molecule PLX-3618 Deposited 2026-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 44–165（122 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1C4W PLX-3618 × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；0.2 M ammonium sulfate, 0.10 M Tris/HCl pH 8.10, 35.00% w/v PEG 3350
Resolution 1.66 Å R-free 0.202
9ZYT Crystal Structure of BRD4 Bromodomain BD1 in Complex with Small Molecule PLX-3618 Deposited 2026-01-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain BBB 44–165（122 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1C4W PLX-3618 × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；0.2 M ammonium sulfate, 0.10 M Tris/HCl pH 8.10, 35.00% w/v PEG 3350
Resolution 1.66 Å R-free 0.202

601 other PDB entries and 778 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRD4_HUMAN
Isoform O60885-3
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–127； UniProt 42–168

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6bn9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6bn9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6bn9
Deposition date deposition_date2017-11-16
Structure title titleCrystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC
Keywords keywordsPROTAC, degrader, E3 ligase, CRBN, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.40 Å
Radius of gyration Rg (electron density) rg_electron38.19 Å
Forward intensity I(0) i0322669000.00
Molecular weight molecular_weight146790.0 kDa
Excluded volume excluded_volume184140 ų
Envelope volume envelope_volume245320 ų
Hydration-shell volume shell_volume54444 ų
Envelope diameter envelope_diameter139.3 Å
Shell Rg shell_rg43.14 Å
Envelope Rg envelope_rg38.39 Å
Shape Rg shape_rg38.20 Å
Total Rg total_rg38.48 Å
Total atoms total_atoms10314
Residues n_residues1310
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax132.3 Å
Rg (real space) rg_real38.63 Å
Rg uncertainty (real space) rg_real_error1.08 Å
I(0) (real space) i0_real3.2270e+08
I(0) uncertainty (real space) i0_real_error5.3780e+06
Rg (reciprocal space) rg_reciprocal38.49 Å
I(0) (reciprocal space) i0_reciprocal322600000.0000
Solution quality estimate total_estimate0.8436
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.0 Å
Skewness Skewness skewness0.547
Kurtosis Kurtosis kurtosis-0.064
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82230000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.765; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.692
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)