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2dat

Solution structure of the Bromodomain of human SWI/SNF related matrix associated actin dependent regulator of cromatin subfamily A member 2

Method: SOLUTION NMR Dmax: 61.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Possible global transcription activator SNF2L2

Homo sapiens

UniProt P51531

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 1373–1482 Fragment：Bromodomain No other associated polymer 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

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 2DAT Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 method 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 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 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 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 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 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 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 method 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 method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 method 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 method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 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 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 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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
9QAC Crystal structure of the SMARCA2 bromodomain bound to a fragment screening hit Deposited 2025-02-28 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 1373–1493（121 aa）
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
9QAC Crystal structure of the SMARCA2 bromodomain bound to a fragment screening hit Deposited 2025-02-28 Different construct 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 1373–1493（121 aa）
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
9QAC Crystal structure of the SMARCA2 bromodomain bound to a fragment screening hit Deposited 2025-02-28 Different construct Different ligand/ion Different experimental method 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 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
9QAD Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17) Deposited 2025-02-28 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 1373–1493（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 construct 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 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 construct Different ligand/ion Different experimental method 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 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 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 62 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SMCA2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–117； UniProt 1373–1482

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 2dat

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2dat
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2dat
Deposition date deposition_date2005-12-14
Structure title titleSolution structure of the Bromodomain of human SWI/SNF related matrix associated actin dependent regulator of cromatin subfamily A member 2
Keywords keywords;Bromodomain, all alpha protein, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSCRIPTION ;; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.12 Å
Radius of gyration Rg (electron density) rg_electron15.55 Å
Forward intensity I(0) i01086620000.00
Molecular weight molecular_weight276980.0 kDa
Excluded volume excluded_volume346320 ų
Envelope volume envelope_volume42407 ų
Hydration-shell volume shell_volume18373 ų
Envelope diameter envelope_diameter65.3 Å
Shell Rg shell_rg26.02 Å
Envelope Rg envelope_rg20.84 Å
Shape Rg shape_rg15.53 Å
Total Rg total_rg15.79 Å
Total atoms total_atoms39200
Residues n_residues2460
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 dmax61.9 Å
Rg (real space) rg_real16.15 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real1.0870e+09
I(0) uncertainty (real space) i0_real_error1.2610e+07
Rg (reciprocal space) rg_reciprocal16.14 Å
I(0) (reciprocal space) i0_reciprocal1087000000.0000
Solution quality estimate total_estimate0.7200
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.2 Å
Skewness Skewness skewness0.404
Kurtosis Kurtosis kurtosis-0.032
Angular range angular_range— – 0.4950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha382700.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.549; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.708; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2data1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.2 — Bromodomain
Family Family familya.29.2.0 — automated matches
Domain ID domain_idd2data2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2data3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2datA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
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8. Citations (1)

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9. Files and Curves (10)