4z6i

Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand

Method: X-RAY DIFFRACTION D_max: 84.1 Å Quality: REASONABLE

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Bromodomain-containing protein 9

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 14–134	Fragment：unp residues 14-134	4L3 tert-butyl [(2R,3S)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxo-2-phenylpiperidin-3-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；0.1M MMT pH6, 30% PEG 1k	Resolution 1.95 Å R-free 0.230
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 14–134	Fragment：unp residues 14-134	4L3 tert-butyl [(2R,3S)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxo-2-phenylpiperidin-3-yl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；277.15 K；0.1M MMT pH6, 30% PEG 1k	Resolution 1.95 Å R-free 0.230

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 4Z6I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21GE Solution structures of BRD9 bromodomain in complex with histone H3 acetyl-lysine 18 (H3K18ac) peptide Deposited 2025-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–250（117 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) Null；Pressure 1 NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
21HJ Solution structures of BRD9 bromodomain in complex with histone H3 lactyl-lysine 18 (H3K18la) peptide Deposited 2025-12-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 134–250（117 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) null；Pressure 1 NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 500 mM sodium chloride, 2.7 mM potassium chloride, 10 mM sodium phosphate, 1.8 mM potassium phosphate, 2 mM DTT, 100% D2O \| 100% D2O	Resolution not provided
3HME Crystal structure of human bromodomain containing 9 isoform 1 (BRD9) Deposited 2009-05-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Fragment：Bromodomain, UNP RESIDUES 14-134 Chain B 14–134（121 aa） Fragment：Bromodomain, UNP RESIDUES 14-134	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25.5% PEG 3350, 0.17M (NH4)2SO4, 15% glyc, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.23 Å R-free 0.263
4UIV BROMODOMAIN OF HUMAN BRD9 WITH N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4- oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c-pyridine-2- carboximidamide Deposited 2015-04-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–238（105 aa） Fragment：BROMODOMAIN OF BRD9, UNP RESIDUES 134-238	Not recorded	EDO 1,2-ETHANEDIOL × 1 XZB N-(1,1-dioxo-1-thian-4-yl)-5-methyl-4-oxo-7-3-(trifluoromethyl)phenyl-4H,5H-thieno-3,2-c-pyridine-2-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；277 K；0.1M MORPHEUS BUFFER PH 6.5, 30% MORPHEUS_EDO_P8K,0.1M MORPHEUS AMINO ACIDS 4C	Resolution 1.72 Å R-free 0.173
4XY8 Crystal Structure of the bromodomain of BRD9 in complex with a 2-amine-9H-purine ligand Deposited 2015-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：UNP residues 14-134	Not recorded	43U 6-(5-bromo-2-methoxyphenyl)-9H-purin-2-amine × 1 BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.20M NaBr, 0.1M BTProp pH 7.5, 20.0% PEG 3350, 10.0% EtGly,	Resolution 1.70 Å R-free 0.186
4YY4 Crystal structure of BRD9 Bromodomain bound to DMSO Deposited 2015-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES, pH 7.5, 25% w/v PEG3350	Resolution 1.47 Å R-free 0.234
4YY6 Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；277 K；0.2 M sodium malonate, pH 4.0, 20% w/v PEG3350	Resolution 1.45 Å R-free 0.208
4YYD Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M sodium malonate, pH 7.0, 20% w/v PEG3350	Resolution 1.52 Å R-free 0.226
4YYG Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05 M calcium chloride dihydrate, 0.1 M Bis-Tris, pH 6.5, 30% v/v PEG550 MME	Resolution 2.10 Å R-free 0.311
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350	Resolution 1.74 Å R-free 0.260
4YYH Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M sodium citrate, pH 5.5, 0.2 M sodium chloride, 20% w/v PEG3350	Resolution 1.74 Å R-free 0.260
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain B 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350	Resolution 1.50 Å R-free 0.242
4YYI Crystal structure of BRD9 Bromodomain bound to an acetylated peptide Deposited 2015-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain E 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M Bis-Tris, pH 6.5, 25% w/v PEG3350	Resolution 1.50 Å R-free 0.242
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain B 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350	Resolution 1.85 Å R-free 0.244
4YYJ Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain E 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M ammonium chloride, 20% w/v PEG3350	Resolution 1.85 Å R-free 0.244
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain B 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME	Resolution 1.79 Å R-free 0.261
4YYK Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide Deposited 2015-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123) Chain E 17–123（107 aa） Fragment：bromodomain (UNP residues 17-123)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES, pH 6.5, 15% w/v PEG550 MME	Resolution 1.79 Å R-free 0.261
4Z6H Crystal structure of BRD9 bromodomain in complex with a valerolactam quinolone ligand Deposited 2015-04-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：unp residues 14-134	Not recorded	4L2 1,4-dimethyl-7-(2-oxopiperidin-1-yl)quinolin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；0.1 M PCB pH 8, 30% PEG1K	Resolution 1.80 Å R-free 0.271
4Z6H Crystal structure of BRD9 bromodomain in complex with a valerolactam quinolone ligand Deposited 2015-04-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：unp residues 14-134	Not recorded	4L2 1,4-dimethyl-7-(2-oxopiperidin-1-yl)quinolin-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277.15 K；0.1 M PCB pH 8, 30% PEG1K	Resolution 1.80 Å R-free 0.271
5E9V Crystal structure of BRD9 bromodomain in complex with an indolizine ligand Deposited 2015-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Fragment：UNP residues 14-134 Chain B 14–134（121 aa） Fragment：UNP residues 14-134	Not recorded	5L0 1-[1-(imidazo[1,2-a]pyridin-5-yl)-7-(morpholin-4-yl)indolizin-3-yl]ethanone × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.2 M NaNO3, 0.1 M BTProp pH 6.5, 20% PEG 3350, 10% EtGly	Resolution 1.80 Å R-free 0.231
5EU1 CRYSTAL STRUCTURE OF BRD9 IN COMPLEX WITH BI-7273 Deposited 2015-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：UNP residues 14-134	Not recorded	5SW 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；30 % glycerol ethoxylate, 0.1 M Tris	Resolution 1.60 Å R-free 0.192
5EU1 CRYSTAL STRUCTURE OF BRD9 IN COMPLEX WITH BI-7273 Deposited 2015-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：UNP residues 14-134	Not recorded	5SW 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；30 % glycerol ethoxylate, 0.1 M Tris	Resolution 1.60 Å R-free 0.192
5F1H Crystal structure of the BRD9 bromodamian in complex with BI-9564. Deposited 2015-11-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：Bromodomain, UNP residues 14-134	Not recorded	5U6 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.82 Å R-free 0.202
5F1H Crystal structure of the BRD9 bromodamian in complex with BI-9564. Deposited 2015-11-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：Bromodomain, UNP residues 14-134	Not recorded	5U6 4-[4-[(dimethylamino)methyl]-2,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.82 Å R-free 0.202
5F1L Crystal structure of the bromodomain of BRD9 in complex with compound 9. Deposited 2015-11-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：Bromodomain, UNP residues 14-134	Not recorded	5U2 5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 2.30 Å R-free 0.209
5F1L Crystal structure of the bromodomain of BRD9 in complex with compound 9. Deposited 2015-11-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：Bromodomain, UNP residues 14-134	Not recorded	5U2 5-[3,5-dimethoxy-4-[(3-oxidanylazetidin-1-yl)methyl]phenyl]-1,3-dimethyl-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 2.30 Å R-free 0.209
5F25 Crystal structure of the BRD9 bromodomain in complex with compound 4. Deposited 2015-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：bromodomain	Not recorded	5TU 4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.68 Å R-free 0.205
5F25 Crystal structure of the BRD9 bromodomain in complex with compound 4. Deposited 2015-12-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：bromodomain	Not recorded	5TU 4-(1,5-dimethyl-6-oxidanylidene-pyridin-3-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.68 Å R-free 0.205
5F2P Crystal structure of the BRD9 bromodomain in complex with compound 3. Deposited 2015-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa） Fragment：bromodomain	Not recorded	5TY 2-(dimethylamino)-6-methyl-pyrido[4,3-d]pyrimidin-5-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.80 Å R-free 0.220
5F2P Crystal structure of the BRD9 bromodomain in complex with compound 3. Deposited 2015-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa） Fragment：bromodomain	Not recorded	5TY 2-(dimethylamino)-6-methyl-pyrido[4,3-d]pyrimidin-5-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；glycerol ethoxylate, Tris	Resolution 1.80 Å R-free 0.220
5I40 BRD9 in complex with Cpd1 (6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one) Deposited 2016-02-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 138–239（102 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 67N 6-methyl-1,6-dihydro-7H-pyrrolo[2,3-c]pyridin-7-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.1 K；0.2 M sodium formate 10-15% PEG3350	Resolution 1.04 Å R-free 0.160
5I7X BRD9 in complex with Cpd2 (N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide) Deposited 2016-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 138–238（101 aa）	Not recorded	67B N,N-dimethyl-3-(6-methyl-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)benzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether	Resolution 1.18 Å R-free 0.168
5I7Y BRD9 in complex with Cpd4 ((E)-3-(6-(but-2-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide) Deposited 2016-02-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 138–238（101 aa）	Not recorded	69G 3-{6-[(2E)-but-2-en-1-yl]-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl}-N,N-dimethylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether	Resolution 1.45 Å R-free 0.187
5IGM Crystal structure of the bromodomain of human BRD9 in complex with bromosporine (BSP) Deposited 2016-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Fragment：UNP Residues 14-134 Chain B 14–134（121 aa） Fragment：UNP Residues 14-134	Not recorded	BMF Bromosporine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M bis tris pH 5.5, 0.2 M sodium chloride, 25% PEG3350	Resolution 1.60 Å R-free 0.266
5IGN Crystal structure of human BRD9 bromodomain in complex with LP99 chemical probe Deposited 2016-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Fragment：UNP residues 14-134 Chain B 14–134（121 aa） Fragment：UNP residues 14-134	Not recorded	6B2 N-[(2R,3S)-2-(4-chlorophenyl)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxopiperidin-3-yl]-2-methylpropane-1-sulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M sodium nitrate, 0.1 M bis tris propane pH 8.5, 20% PEG 3350, 10% ethylene glycol	Resolution 1.70 Å R-free 0.243
5JI8 Crystal structure of the BRD9 bromodomain and hit 1 Deposited 2016-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 137–239（103 aa） Fragment：UNP residues 137-239	Not recorded	6KT 2-amino-1,3-benzothiazole-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；0.1M Bis-Tris PH6.4, 27% PEG 3350	Resolution 1.42 Å R-free 0.170
5MKY BROMODOMAIN OF HUMAN BRD9 WITH 4-chloro-2-methyl-5-((2-methyl-1,2,3,4-tetrahydroisoquinolin-5-yl)amino)pyridazin-3(2H)-one Deposited 2016-12-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–238（105 aa）	Not recorded	I0D 4-chloranyl-2-methyl-5-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-5-yl)amino]pyridazin-3-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus condition 54 - 0.1M morpheus buffer 2 pH 7.5, 30% morpheus_EDO_P8K, 0.1M Morpheus ethylene glycols	Resolution 1.67 Å R-free 0.220
5TWX Crystal Structure of BRD9 bromodomain Deposited 2016-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–250（117 aa） Fragment：UNP residues 134-250	Not recorded	7P7 N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000	Resolution 2.55 Å R-free 0.280
5TWX Crystal Structure of BRD9 bromodomain Deposited 2016-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 134–250（117 aa） Fragment：UNP residues 134-250	Not recorded	7P7 N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000	Resolution 2.55 Å R-free 0.280
5TWX Crystal Structure of BRD9 bromodomain Deposited 2016-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 134–250（117 aa） Fragment：UNP residues 134-250	Not recorded	7P7 N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000	Resolution 2.55 Å R-free 0.280
5TWX Crystal Structure of BRD9 bromodomain Deposited 2016-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 134–250（117 aa） Fragment：UNP residues 134-250	Not recorded	7P7 N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000	Resolution 2.55 Å R-free 0.280
5TWX Crystal Structure of BRD9 bromodomain Deposited 2016-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 134–250（117 aa） Fragment：UNP residues 134-250 Chain B 134–250（117 aa） Fragment：UNP residues 134-250 Chain C 134–250（117 aa） Fragment：UNP residues 134-250 Chain D 134–250（117 aa） Fragment：UNP residues 134-250	Not recorded	7P7 N-[6-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)hexyl]-2-(4-{2-[N-(1,1-dioxo-1lambda~6~-thian-4-yl)carbamimidoyl]-5-methyl-4-oxo-4,5-dihydrothieno[3,2-c]pyridin-7-yl}-2-methoxyphenoxy)acetamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000	Resolution 2.55 Å R-free 0.280
6BQA BRD9 bromodomain in complex with 3-(6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl)-N,N-dimethylbenzamide Deposited 2017-11-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 138–239（102 aa） Fragment：BRD9 bromodomain	Not recorded	67C 3-[6-(but-3-en-1-yl)-7-oxo-6,7-dihydro-1H-pyrrolo[2,3-c]pyridin-4-yl]-N,N-dimethylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；0.1M Bis-Tris, pH 6.5, 20% PEG 2000 monomethylether	Resolution 1.03 Å R-free 0.171
6HM0 Crystal structure of human BRD9 bromodomain in complex with a PROTAC Deposited 2018-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	GBW (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；24% PEG 3350 0.2 M NH4F	Resolution 2.40 Å R-free 0.251
6HM0 Crystal structure of human BRD9 bromodomain in complex with a PROTAC Deposited 2018-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	GBW (2~{S},4~{S})-1-[(2~{S})-2-[2-[2-[2-[4-[[2,6-dimethoxy-4-(2-methyl-1-oxidanylidene-2,7-naphthyridin-4-yl)phenyl]methyl]piperazin-1-yl]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；24% PEG 3350 0.2 M NH4F	Resolution 2.40 Å R-free 0.251
6UZF Crystal structure of the unliganded bromodomain of human BRD9 Deposited 2019-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；0.05 M (NH4)2SO4, 0.05 M Bis-Tris (pH 6.5), 30% Pentaerythritol ethoxylate (15/4 EO/OH)	Resolution 1.75 Å R-free 0.219
6V0S Crystal structure of the bromodomain of human BRD9 bound to TG003 Deposited 2019-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Chain B 14–134（121 aa）	Not recorded	EAE (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；291 K；0.2 M Li2SO4, 0.1 M HEPES (pH 7.5), 25% w/v PEG 3,350	Resolution 2.40 Å R-free 0.230
6V0X Crystal structure of the bromodomain of human BRD9 bound to sunitinib Deposited 2019-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	B49 N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo xamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), and 25% PEG 3350	Resolution 1.50 Å R-free 0.223
6V14 Crystal structure of the bromodomain of human BRD9 bound to TP472 Deposited 2019-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	QMG 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), and 25% PEG 3350	Resolution 1.70 Å R-free 0.171
6V1B Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 Deposited 2019-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 H1B N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M KSCN, 30% w/v PEG MME 2,000	Resolution 1.35 Å R-free 0.203
6V1B Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 Deposited 2019-11-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	H1B N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M KSCN, 30% w/v PEG MME 2,000	Resolution 1.35 Å R-free 0.203
6V1B Crystal structure of the bromodomain of human BRD9 bound to I-BRD9 Deposited 2019-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–134（121 aa） Chain B 14–134（121 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 H1B N'-[1,1-bis(oxidanylidene)thian-4-yl]-5-ethyl-4-oxidanylidene-7-[3-(trifluoromethyl)phenyl]thieno[3,2-c]pyridine-2-carboximidamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M KSCN, 30% w/v PEG MME 2,000	Resolution 1.35 Å R-free 0.203
6Y7H Structure of the BRD9 bromodomain and compound 11 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	OFK 1-(8-phenylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05M ammonium sulfate, 30% pentaerythritol ethoxylate 15/4, 0.1M bis-tris pH 6.5	Resolution 1.80 Å R-free 0.226
6Y7H Structure of the BRD9 bromodomain and compound 11 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	OFK 1-(8-phenylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.05M ammonium sulfate, 30% pentaerythritol ethoxylate 15/4, 0.1M bis-tris pH 6.5	Resolution 1.80 Å R-free 0.226
6Y7I Structure of the BRD9 bromodomain and compound 2 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	OF8 1-(8-pyridin-2-ylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.02M sodium/potassium phosphate	Resolution 1.60 Å R-free 0.215
6Y7I Structure of the BRD9 bromodomain and compound 2 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	OF8 1-(8-pyridin-2-ylpyrrolo[1,2-a]pyrimidin-6-yl)ethanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.02M sodium/potassium phosphate	Resolution 1.60 Å R-free 0.215
6Y7J Structure of the BRD9 bromodomain and compound 15 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	OF5 1-[8-(2,5-dimethoxyphenyl)pyrrolo[1,2-a]pyrimidin-6-yl]ethanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES pH 7.5	Resolution 1.60 Å R-free 0.244
6Y7J Structure of the BRD9 bromodomain and compound 15 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	OF5 1-[8-(2,5-dimethoxyphenyl)pyrrolo[1,2-a]pyrimidin-6-yl]ethanone × 1 ACT ACETATE ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M ammonium acetate, 25% PEG3350, 0.1M HEPES pH 7.5	Resolution 1.60 Å R-free 0.244
6Y7K Structure of the BRD9 bromodomain and compound 27 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	OEZ ~{N}-cyclobutyl-3-(6-ethanoylpyrrolo[1,2-a]pyrimidin-8-yl)-4-methoxy-benzamide × 1 EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350,10% ethylene glycol, 0.1M bis-tris-propane pH 7.5, 0.2M potassium thiocyanate	Resolution 1.20 Å R-free 0.158
6Y7L Structure of the BRD9 bromodomain and TP-472 Deposited 2020-03-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	QMG 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M sodium chloride, 25% PEG3350, 0.1M tris pH 8.5	Resolution 1.80 Å R-free 0.190
6YQR BRD9 with Biphenyl-methylamino-dimethylpyridazinone Deposited 2020-04-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 134–238（105 aa）	Not recorded	P8W 2,4-dimethyl-5-[(2-phenylphenyl)methylamino]pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.10M morpheus buffer 1 (1M pH 6.5), 30.00% morpheus EDO_P8K (60%) 0.10M Morpheus Amino Acids (1M)	Resolution 1.68 Å R-free 0.185
6YQS BRD9 with methylpiperazinyl-benzyl-amino-dimethylpyridazinone Deposited 2020-04-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 134–238（105 aa）	Not recorded	P8Z 2,4-dimethyl-5-[[2-(4-methylpiperazin-1-yl)phenyl]methylamino]pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.03M NaF, 0.03M NaI, 0.03M NaBr, 0.10M morpheus buffer 3 (1M pH 8.5), 37.5% morpheus MPD_P1K_3350	Resolution 1.68 Å R-free 0.201
6YQW BRD9 with 4-chloro-2-methyl-methylamino-pyridazinone Deposited 2020-04-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–238（105 aa）	Not recorded	82I 4-chloranyl-2-methyl-5-(methylamino)pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M morpheus buffer 3, pH 8.5, 30% morpheus_EDO_p8K, 0.1M morpheus alcohol	Resolution 1.50 Å R-free 0.276
8A7I Crystal structure of BRD9 bromodomain in complex with compound EA-89 Deposited 2022-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–240（111 aa）	Not recorded	L8L ~{N}-[1,1-bis(oxidanylidene)thian-4-yl]-7-[3-methyl-1-(piperidin-4-ylmethyl)indol-5-yl]-4-oxidanylidene-5-propyl-thieno[3,2-c]pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；15% PEG 3350, 0.1M Succinic Acid	Resolution 1.76 Å R-free 0.237
8A7I Crystal structure of BRD9 bromodomain in complex with compound EA-89 Deposited 2022-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 130–240（111 aa）	Not recorded	L8L ~{N}-[1,1-bis(oxidanylidene)thian-4-yl]-7-[3-methyl-1-(piperidin-4-ylmethyl)indol-5-yl]-4-oxidanylidene-5-propyl-thieno[3,2-c]pyridine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；15% PEG 3350, 0.1M Succinic Acid	Resolution 1.76 Å R-free 0.237
8AHC Crystal structure of the BRD9 bromodomain with BI-7189 Deposited 2022-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 14–134（121 aa）	Not recorded	M2O [2,6-dimethoxy-4-(1,2,5-trimethyl-6-oxidanylidene-pyridin-3-yl)phenyl]methyl-dimethyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.44；277 K；100 mM Tris 28% glycerol ethoxylate	Resolution 1.50 Å R-free 0.230
8AHC Crystal structure of the BRD9 bromodomain with BI-7189 Deposited 2022-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–134（121 aa）	Not recorded	M2O [2,6-dimethoxy-4-(1,2,5-trimethyl-6-oxidanylidene-pyridin-3-yl)phenyl]methyl-dimethyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.44；277 K；100 mM Tris 28% glycerol ethoxylate	Resolution 1.50 Å R-free 0.230
9DU1 Co-crystal structure of the ternary complex of human FKBP12, BRD9 bromo domain and Compound 1 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 × 8 PDB declaration: octameric	Chain E 130–240（111 aa） Chain F 130–240（111 aa） Chain G 130–240（111 aa） Chain H 130–240（111 aa）	Not recorded	A1BB8 4-[4-{cyclopropyl[(1-methyl-1H-pyrazol-4-yl)methyl]amino}-6-({1-[(2R)-2-{[(2S)-1-(3,3-dimethyl-2-oxopentanoyl)piperidine-2-carbonyl]amino}-4-(4-methoxyphenyl)butanoyl]piperidin-4-yl}amino)-1,3,5-triazin-2-yl]-N-ethylpiperazine-1-carboxamide × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1 M HEPES PH 7.5, 20% PEG 8000 (MCSG SCREEN 1, CONDITION A1); 1:1:1 FKBP12:BRD9:MOTHER LIQUOR PLUS EQUIMOLAR COMPOUND IN 200-NL DROP. COMPLEX CONCENTRATED TO 10 MG/ML	Resolution 2.01 Å R-free 0.259
9KLA Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22024 Deposited 2024-11-14	Different construct 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 134–239（106 aa）	Not recorded	A1EF0 1-[1-(3,5-dimethoxyphenyl)indolizin-3-yl]ethanone × 4 GOL GLYCEROL × 2 MLT D-MALATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350	Resolution 1.78 Å R-free 0.232
9KLY Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22032 Deposited 2024-11-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 134–239（106 aa）	Not recorded	A1EHA 1-[1-[2,5-dimethoxy-4-[(1~{S})-1-oxidanylethyl]phenyl]indolizin-3-yl]ethanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.15 Å R-free 0.227
9KM1 Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22077 Deposited 2024-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 134–239（106 aa） Chain B 134–239（106 aa）	Not recorded	A1EFZ 1-[1-[4-(imidazol-1-ylmethyl)-3,5-dimethoxy-phenyl]indolizin-3-yl]propan-1-one × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.68 Å R-free 0.300
9LKR Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22076 Deposited 2025-01-16	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 134–239（106 aa） Chain B 134–239（106 aa）	Not recorded	A1EKN 1-[1-[4-(imidazol-1-ylmethyl)-3,5-dimethoxy-phenyl]indolizin-3-yl]ethanone × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.68 Å R-free 0.328

50 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BRD9_HUMAN
Isoform	Q9H8M2-1
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–123； UniProt 14–134 Author chain B； PDBConstruct 3–123； UniProt 14–134

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4z6i
Deposition date deposition_date	2015-04-05
Structure title title	Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand
Keywords keywords	;lysine-acetylated histone binding, chromatin regulator, transcription, Bromodomain, Structural Genomics, Structural Genomics Consortium, SGC ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.04 Å
Radius of gyration Rg (electron density) rg_electron	22.92 Å
Forward intensity I(0) i0	11843600.00
Molecular weight molecular_weight	27184.0 kDa
Excluded volume excluded_volume	34643 Å³
Envelope volume envelope_volume	40441 Å³
Hydration-shell volume shell_volume	16576 Å³
Envelope diameter envelope_diameter	85.7 Å
Shell Rg shell_rg	27.43 Å
Envelope Rg envelope_rg	23.13 Å
Shape Rg shape_rg	22.95 Å
Total Rg total_rg	23.48 Å
Total atoms total_atoms	1908
Residues n_residues	226
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	84.1 Å
Rg (real space) rg_real	23.37 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.1840e+07
I(0) uncertainty (real space) i0_real_error	1.9340e+05
Rg (reciprocal space) rg_reciprocal	23.29 Å
I(0) (reciprocal space) i0_reciprocal	11840000.0000
Solution quality estimate total_estimate	0.7499
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.656
Kurtosis Kurtosis kurtosis	-0.117
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5409000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.466; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.397; Smooth: 0.957

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bromodomain-containing protein 9
Molecular weight formula_weight	14249.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2019

SMLKLSAENESTPIQQLLEHFLRQLQRKDPHGFFAFPVTDAIAPGYSMIIKHPMDFGTMKDKIVANEYKSVTEFKADFKLMCDNAMTYNRPDTVYYKLAKKILHAGFKMMSKERLLALKRSMS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	tert-butyl [(2R,3S)-1-(1,4-dimethyl-2-oxo-1,2-dihydroquinolin-7-yl)-6-oxo-2-phenylpiperidin-3-yl]carbamate
Molecular weight formula_weight	461.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4z6ia_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

Domain ID domain_id	d4z6ib_
Class class	a — All alpha proteins
Fold Fold fold	a.29 — Bromodomain-like
Superfamily Superfamily superfamily	a.29.2 — Bromodomain
Family Family family	a.29.2.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4z6iA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

Domain ID domain_id	4z6iB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily	10 — Bromodomain-like

▶

8. Citations (1)

▶

Unit-cell length a length_a	60.015 Å
Unit-cell length b length_b	29.458 Å
Unit-cell length c length_c	141.187 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.24 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	28.840 Å
R factor r_factor	0.1837
R_work r_work	0.1812
R_free r_free	0.2299

fit	/app/data/saxs_computation/z6/4z6i/4z6i.fit
pddf	/app/data/pr_computation/z6/4z6i/4z6i.pr.out
profile	/app/data/saxs_computation/z6/4z6i/4z6i.dat