Probable global transcription activator SNF2L2
Homo sapiens
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1373–1493 | Not recorded | A1I5P methyl 2-azanyl-1~{H}-indole-3-carboxylate × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7.0 | Resolution 2.07 Å R-free 0.220 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1373–1493 | Not recorded | A1I5P methyl 2-azanyl-1~{H}-indole-3-carboxylate × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7.0 | Resolution 2.07 Å R-free 0.220 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 1373–1493 | Not recorded | A1I5P methyl 2-azanyl-1~{H}-indole-3-carboxylate × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7.0 | Resolution 2.07 Å R-free 0.220 |
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 9QAC | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2DAT Solution structure of the Bromodomain of human SWI/SNF related matrix associated actin dependent regulator of cromatin subfamily A member 2 Deposited 2005-12-14 | Different construct 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
1373–1482（110 aa）
Fragment：Bromodomain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 195mM；Pressure ambient
NMR sample composition
1.39mM Bromodomain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 75mM Guanidine oxalate; 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 5DKC Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3 chemical probe Deposited 2015-09-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
Fragment：UNP residues 1373-1493
|
Not recorded | ZN ZINC ION × 1 5BW (2E)-1-(2-hydroxyphenyl)-3-[(1R,4R)-5-(pyridin-2-yl)-2,5-diazabicyclo[2.2.1]hept-2-yl]prop-2-en-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；19% PEG 6K, 4% ethyleneglycol, 0.01M ZnCl2
|
Resolution 1.60 Å R-free 0.211 |
| 5DKH Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17 Deposited 2015-09-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
Fragment：UNP residues 1373-1493
|
Not recorded | ZN ZINC ION × 2 5C0 (2E)-3-[(6S,9R)-4-(cyclopropylamino)-6,7,8,9-tetrahydro-5H-6,9-epiminocyclohepta[d]pyrimidin-10-yl]-1-(2-hydroxyphenyl)prop-2-en-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；20% PEG 6K, 10% ethyleneglycol, 0.1 Hepes pH 7, 0.01M ZnCl2
|
Resolution 1.70 Å R-free 0.241 |
| 5DKH Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17 Deposited 2015-09-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
Fragment：UNP residues 1373-1493
|
Not recorded | ZN ZINC ION × 2 5C0 (2E)-3-[(6S,9R)-4-(cyclopropylamino)-6,7,8,9-tetrahydro-5H-6,9-epiminocyclohepta[d]pyrimidin-10-yl]-1-(2-hydroxyphenyl)prop-2-en-1-one × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；20% PEG 6K, 10% ethyleneglycol, 0.1 Hepes pH 7, 0.01M ZnCl2
|
Resolution 1.70 Å R-free 0.241 |
| 5DKH Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a hydroxyphenyl propenone inhibitor 17 Deposited 2015-09-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
Fragment：UNP residues 1373-1493
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；20% PEG 6K, 10% ethyleneglycol, 0.1 Hepes pH 7, 0.01M ZnCl2
|
Resolution 1.70 Å R-free 0.241 |
| 6EG2 Crystal structure of human BRM in complex with compound 16 Deposited 2018-08-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
705–955（251 aa）
|
Not recorded | J7J N-(5-amino-2-chloropyridin-4-yl)-N'-(4-bromo-3-{[3-(hydroxymethyl)phenyl]ethynyl}-1,2-thiazol-5-yl)urea × 2 IPA ISOPROPYL ALCOHOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；100mM Hepes pH7.5, 200mM sodium chloride, 8% isopropanol
|
Resolution 2.98 Å R-free 0.304 |
| 6EG3 Crystal structure of human BRM in complex with compound 15 Deposited 2018-08-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
705–955（251 aa）
|
Not recorded | J7G 3-[(4-{[(2-chloropyridin-4-yl)carbamoyl]amino}pyridin-2-yl)ethynyl]benzoic acid × 1 EOH ETHANOL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；100mM Tris pH7, 14% Ethanol
|
Resolution 2.84 Å R-free 0.267 |
| 6HAX Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | 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
1373–1493（121 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；13% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 8.0
|
Resolution 2.35 Å R-free 0.268 |
| 6HAX Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | 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
1373–1493（121 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 FWZ (2~{S},4~{R})-~{N}-[[2-[2-[4-[[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]methyl]phenyl]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；13% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 8.0
|
Resolution 2.35 Å R-free 0.268 |
| 6HAY Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | 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
1373–1493（121 aa）
|
Not recorded | FX8 (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 11 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75
|
Resolution 2.24 Å R-free 0.223 |
| 6HAY Crystal structure of PROTAC 1 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2018-08-09 | 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
1373–1493（121 aa）
|
Not recorded | FX8 (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[3-azanyl-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 11 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.75；277 K；18% (w/v) PEG 3350, 0.2 M sodium formate, 0.1 M HEPES, pH 7.75
|
Resolution 2.24 Å R-free 0.223 |
| 6HAZ Crystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand Deposited 2018-08-09 | 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
1373–1493（121 aa）
Chain B
1373–1493（121 aa）
|
Not recorded | FX5 2-(6-azanyl-5-piperazin-4-ium-1-yl-pyridazin-3-yl)phenol × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；25% (w/v) PEG 6000, 0.1 M HEPES, pH 6.1, 0.01M zinc chloride, 0.01 M cobalt (III) hexamine chloride, 8% (v/v) ethylene glycol
|
Resolution 1.31 Å R-free 0.193 |
| 7Z6L Crystal structure of PROTAC 5 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-12 | 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
1373–1493（121 aa）
|
Not recorded | IEI (2~{S},4~{R})-~{N}-[[2-[3-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；33% (v/v) glycerol ethoxylate, 0.2 M ammonium chloride, 0.1 M HEPES, pH 7.5
|
Resolution 2.24 Å R-free 0.232 |
| 7Z76 Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | 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
1373–1493（121 aa）
|
Not recorded | IOD IODIDE ION × 7 IFJ (2~{S},4~{R})-~{N}-[(1~{R})-2-[(2~{R})-1-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propan-2-yl]oxy-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；14.5 % PEG 3350, 0.1 M BIS-TRIS propane pH 5.8, 100 mM sodium iodide
|
Resolution 1.32 Å R-free 0.202 |
| 7Z77 Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | 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
1373–1493（121 aa）
|
Not recorded | IFF (2~{S},4~{R})-~{N}-[(1~{S})-4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]butyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20 % PEG 3350, 0.1 M BIS_TRIS propane pH 7.5, 200 mM sodium formate
|
Resolution 1.97 Å R-free 0.251 |
| 7Z78 Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | IF8 4-bromanyl-7-cyclopentyl-9-piperidin-4-yl-benzimidazolo[1,2-a]quinazolin-5-one × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% ethylene glycol, 25% PEG 6000, 0.1 M HEPES pH 8.0 and 10 mM zinc chloride
|
Resolution 1.32 Å R-free 0.210 |
| 7Z78 Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | IF8 4-bromanyl-7-cyclopentyl-9-piperidin-4-yl-benzimidazolo[1,2-a]quinazolin-5-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% ethylene glycol, 25% PEG 6000, 0.1 M HEPES pH 8.0 and 10 mM zinc chloride
|
Resolution 1.32 Å R-free 0.210 |
| 7Z78 Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB Deposited 2022-03-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | IF8 4-bromanyl-7-cyclopentyl-9-piperidin-4-yl-benzimidazolo[1,2-a]quinazolin-5-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% ethylene glycol, 25% PEG 6000, 0.1 M HEPES pH 8.0 and 10 mM zinc chloride
|
Resolution 1.32 Å R-free 0.210 |
| 8QJT BRM (SMARCA2) Bromodomain in complex with ligand 10 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 2 VLC 2-[6-azanyl-5-[(1R,5S)-8-[2-(2-methoxyethoxy)pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 6K, 6% ethylene glycol, 10 mM ZnCl2
|
Resolution 2.57 Å R-free 0.263 |
| 8QJT BRM (SMARCA2) Bromodomain in complex with ligand 10 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 VLC 2-[6-azanyl-5-[(1R,5S)-8-[2-(2-methoxyethoxy)pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 6K, 6% ethylene glycol, 10 mM ZnCl2
|
Resolution 2.57 Å R-free 0.263 |
| 8QJT BRM (SMARCA2) Bromodomain in complex with ligand 10 Deposited 2023-09-13 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 VLC 2-[6-azanyl-5-[(1R,5S)-8-[2-(2-methoxyethoxy)pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG 6K, 6% ethylene glycol, 10 mM ZnCl2
|
Resolution 2.57 Å R-free 0.263 |
| 9AYQ SMARCA2 in complex with a pyridine-2-one-based inhibitor Deposited 2024-03-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
495–551（57 aa）
Chain A
701–1150（450 aa）
Chain A
1166–1302（137 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 A1AHQ 4-cyano-N-[1-(2,2-difluoroethyl)-5-fluoro-6-oxo-1,6-dihydropyridin-3-yl]-5-(trifluoromethyl)thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1 uL of protein at a concentration of 28.5 mg/ml in a buffer 25mM Hepes, 300mM NaCl, 5% glycerol, 1mM TCEP, pH 7.5 was combined with 1ul of 0.1 M HEPES, pH 7.1, 4% w/v PEG 8000
|
Resolution 2.90 Å R-free 0.287 |
| 9AYQ SMARCA2 in complex with a pyridine-2-one-based inhibitor Deposited 2024-03-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
495–551（57 aa）
Chain B
701–1150（450 aa）
Chain B
1166–1302（137 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 1 A1AHQ 4-cyano-N-[1-(2,2-difluoroethyl)-5-fluoro-6-oxo-1,6-dihydropyridin-3-yl]-5-(trifluoromethyl)thiophene-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1 uL of protein at a concentration of 28.5 mg/ml in a buffer 25mM Hepes, 300mM NaCl, 5% glycerol, 1mM TCEP, pH 7.5 was combined with 1ul of 0.1 M HEPES, pH 7.1, 4% w/v PEG 8000
|
Resolution 2.90 Å R-free 0.287 |
| 9D11 Smarca2 Bromodomain in complex with compound 22 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 EDO 1,2-ETHANEDIOL × 3 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；32% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 1.68 Å R-free 0.204 |
| 9D11 Smarca2 Bromodomain in complex with compound 22 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；32% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 1.68 Å R-free 0.204 |
| 9D11 Smarca2 Bromodomain in complex with compound 22 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；32% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 1.68 Å R-free 0.204 |
| 9D12 Smarca2 Bromodomain in complex with compound 15 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；28% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 2.10 Å R-free 0.240 |
| 9D12 Smarca2 Bromodomain in complex with compound 15 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；28% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 2.10 Å R-free 0.240 |
| 9D12 Smarca2 Bromodomain in complex with compound 15 Deposited 2024-08-07 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；28% Peg 3350, 50mM ZnAc, 6% Sucrose
|
Resolution 2.10 Å R-free 0.240 |
| 9DTY Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2024-10-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 40 PDB declaration: 40-meric |
Chain A
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain E
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain I
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain M
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain Q
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain U
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain Y
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain c
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain g
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain k
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
|
Not recorded | A1BB4 (4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 10 CIT CITRIC ACID × 5 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.26；291 K；2% v/v Tacsimate, pH 5.0, 0.1 M tri-sodium citrate, pH 5.26, 11.36% w/v PEG3350, 0.1 M barium chloride dihydrate
|
Resolution 3.19 Å R-free 0.285 |
| 9DU0 Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a SMARCA-BD binder Deposited 2024-10-02 | 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
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain B
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
Chain C
1373–1491（119 aa）
Fragment：UNP residues 1373-1491
|
Not recorded | A1BB5 (2P)-2-[(6aS,11R)-6,6a,7,8,9,10-hexahydro-5H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-2-yl]phenol × 2 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.025~0.1 M zinc acetate, 16~26% w/v PEG3350
|
Resolution 3.00 Å R-free 0.338 |
| 9E1K Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 11 Deposited 2024-10-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | A1BF5 (12S)-4-bromo-7,7-dimethyl-9-(piperidin-4-yl)indolo[1,2-a]quinazolin-5(7H)-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.03 M Zinc Acetate
22% v/v PEG 3350
|
Resolution 2.26 Å R-free 0.307 |
| 9E1K Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 11 Deposited 2024-10-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | A1BF5 (12S)-4-bromo-7,7-dimethyl-9-(piperidin-4-yl)indolo[1,2-a]quinazolin-5(7H)-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.03 M Zinc Acetate
22% v/v PEG 3350
|
Resolution 2.26 Å R-free 0.307 |
| 9E1K Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 11 Deposited 2024-10-21 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | A1BF5 (12S)-4-bromo-7,7-dimethyl-9-(piperidin-4-yl)indolo[1,2-a]quinazolin-5(7H)-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.03 M Zinc Acetate
22% v/v PEG 3350
|
Resolution 2.26 Å R-free 0.307 |
| 9E30 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
0.01 M cobalt (III) hexamine chloride
0.1 M HEPES pH 6.1
19% v/v PEG 6000
8% v/v ethylene glycol
|
Resolution 1.71 Å R-free 0.215 |
| 9E30 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
0.01 M cobalt (III) hexamine chloride
0.1 M HEPES pH 6.1
19% v/v PEG 6000
8% v/v ethylene glycol
|
Resolution 1.71 Å R-free 0.215 |
| 9E30 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | A1A1O (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
0.01 M cobalt (III) hexamine chloride
0.1 M HEPES pH 6.1
19% v/v PEG 6000
8% v/v ethylene glycol
|
Resolution 1.71 Å R-free 0.215 |
| 9E31 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 6 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
15% v/v PEG 6000
5.5% v/v ethylene glycol
|
Resolution 1.96 Å R-free 0.238 |
| 9E31 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 6 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
15% v/v PEG 6000
5.5% v/v ethylene glycol
|
Resolution 1.96 Å R-free 0.238 |
| 9E31 Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 6 Deposited 2024-10-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | A1A1P (12'R)-4'-chloro-9'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277.15 K；0.01 M ZnCl2
15% v/v PEG 6000
5.5% v/v ethylene glycol
|
Resolution 1.96 Å R-free 0.238 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain P
1373–1493（121 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain M
1373–1493（121 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain O
1373–1493（121 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYB CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P3 Deposited 2025-01-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
1373–1493（121 aa）
|
Not recorded | A1IYB (2~{S},4~{R})-~{N}-[(1~{R})-2-[2-[4-[4-bromanyl-7-cyclopentyl-5-oxidanylidene-10-[[(2~{S})-oxolan-2-yl]methoxy]-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl]piperidin-1-yl]ethoxy]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-1-[(2~{S})-2-[[1-(dimethylamino)cyclopropyl]carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris propane, 20 % PEG 3350, 0.2 M tri-sodium citrate
|
Resolution 2.84 Å R-free 0.265 |
| 9HYN CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1 Deposited 2025-01-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
1373–1493（121 aa）
|
Not recorded | A1IYO (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M K2HPO4
16 % PEG 8000
0.2 M sodium chloride
|
Resolution 2.37 Å R-free 0.262 |
| 9HYN CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P1 Deposited 2025-01-10 | 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
1373–1493（121 aa）
|
Not recorded | A1IYO (2~{S},4~{R})-~{N}-[[2-[2-[2-[4-[(6-bromanyl-3-methyl-5-oxidanylidene-4~{H}-imidazo[1,2-a]quinazolin-2-yl)methyl]piperazin-1-yl]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M K2HPO4
16 % PEG 8000
0.2 M sodium chloride
|
Resolution 2.37 Å R-free 0.262 |
| 9HYO CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P4 Deposited 2025-01-10 | 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
1373–1493（121 aa）
|
Not recorded | A1IYN (2~{S},4~{R})-~{N}-[[2-[2-[2-[2-[4-[7-(5-bromanyl-4-oxidanylidene-2,3-dihydro-1,3-benzoxazin-2-yl)-4-[cyclopropyl(methyl)amino]-5,6,8,9-tetrahydropyrimido[4,5-d]azepin-2-yl]piperazin-1-yl]ethoxy]ethoxy]ethoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.0
8% ethylene glycol
14% PEG 8K
|
Resolution 3.74 Å R-free 0.348 |
| 9HYP CRYSTAL STRUCTURE OF THE SMARCA2-VCB-COMPLEX WITH PROTAC P5 Deposited 2025-01-10 | 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
1373–1493（121 aa）
|
Not recorded | A1IYM (2~{S},4~{R})-~{N}-[[2-[4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-6~{H}-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]butoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；28% PEG 3350
0.2 M potassium thiocyanate
0.1 M Bis-Tris Propane pH 7.5
|
Resolution 2.20 Å R-free 0.254 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | 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
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | 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
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain I
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain M
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Q
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain U
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain Y
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9MR9 Crystal structure of AU-15330 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB Deposited 2025-01-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain c
1373–1493（121 aa）
|
Not recorded | A1BNT N-({4-[(6M)-3-amino-6-(2-hydroxyphenyl)pyridazin-4-yl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05~0.2 M sodium formate, 0.1 M HEPES, pH 7.5~8.5, 10%~24% w/v PEG3350
|
Resolution 3.30 Å R-free 0.275 |
| 9QAD Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17) Deposited 2025-02-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1373–1493（121 aa）
|
Not recorded | A1I45 5-oxidanyl-2-(phenylmethyl)-1,9-dihydropyrimido[4,5-b]indol-4-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7
|
Resolution 2.08 Å R-free 0.245 |
| 9QAD Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17) Deposited 2025-02-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1373–1493（121 aa）
|
Not recorded | A1I45 5-oxidanyl-2-(phenylmethyl)-1,9-dihydropyrimido[4,5-b]indol-4-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7
|
Resolution 2.08 Å R-free 0.245 |
| 9QAD Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17) Deposited 2025-02-28 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1373–1493（121 aa）
|
Not recorded | A1I45 5-oxidanyl-2-(phenylmethyl)-1,9-dihydropyrimido[4,5-b]indol-4-one × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；277 K；0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7
|
Resolution 2.08 Å R-free 0.245 |
| 9S3R Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB Deposited 2025-07-25 | 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
1373–1493（121 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 |
28 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SMCA2_HUMAN |
| Isoform | P51531-2 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 3–123； UniProt 1373–1493 Author chain B； PDBConstruct 3–123； UniProt 1373–1493 Author chain C； PDBConstruct 3–123； UniProt 1373–1493 |
