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21hj

Solution structures of BRD9 bromodomain in complex with histone H3 lactyl-lysine 18 (H3K18la) peptide

Method: SOLUTION NMR Dmax: 69.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bromodomain-containing protein 9

Homo sapiens

UniProt Q9H8M2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 134–250 Not recorded Histone H3.3C × 1 （Q6NXT2） 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

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 21HJ 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 experimental conditions 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 experimental method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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
4Z6I Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand Deposited 2015-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 14–134（121 aa） Fragment：unp residues 14-134
Not recorded 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
4Z6I Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand Deposited 2015-04-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 14–134（121 aa） Fragment：unp residues 14-134
Not recorded 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
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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 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 method 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 method 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 method 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 method 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 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BRD9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–117； UniProt 134–250

Histone H3.3C

OrganismNot specified

UniProt Q6NXT2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 12–26 Non-standard monomer：Yes (specific site not provided by mmCIF) Bromodomain-containing protein 9 × 1 （Q9H8M2） 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

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 21HJ 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 experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 12–26（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
3KV4 Structure of PHF8 in complex with histone H3 Deposited 2009-11-29 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–25（24 aa） Fragment：UNP Residues 2-25
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 FE2 FE (II) ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 13 OGA N-OXALYLGLYCINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；25% (v/v) polyethylene glycol 3350, 0.2 M NaCl, and 0.1 M NaCitrate pH 5.6, VAPOR DIFFUSION, HANGING DROP
Resolution 2.19 Å R-free 0.255
4Z5T The nucleosome containing human H3.5 Deposited 2015-04-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–135（135 aa）
Chain E 1–135（135 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
Resolution 2.80 Å R-free 0.269
7W67 The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain M 2–10（9 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.19 Å R-free 0.222
7W6I The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3,350
Resolution 2.56 Å R-free 0.244
7W6J The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me2 peptide Deposited 2021-12-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–10（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Resolution 2.68 Å R-free 0.252
7W6L The crystal structure of MLL3-RBBP5-ASH2L in complex with H3K4me0 peptide Deposited 2021-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain M 2–10（9 aa）
Not recorded ZN ZINC ION × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；100 mM sodium cacodylate, pH 6.5, 10% polyethylene glycol 3350, 0.1 M MgCl2
Resolution 2.26 Å R-free 0.223
8Q1G LSD1-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2M, ADA 0.1M,
Resolution 2.60 Å R-free 0.255
8Q1H LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail Deposited 2023-07-31 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 × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2 M, ADA 0.1M
Resolution 2.90 Å R-free 0.254
8Q1J LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–22（21 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartate 1.2 M, ADA 0.1M
Resolution 2.87 Å R-free 0.272
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric
Chain M 1–135（135 aa）
Chain S 1–135（135 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8SR6 Crystal structure of legAS4 from Legionella pneumophila subsp. pneumophila with histone H3 (3-17)peptide Deposited 2023-05-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 4–18（15 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris 6.5 and 38% PPG P400
Resolution 2.22 Å R-free 0.230
8T4F Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL Deposited 2023-06-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 52–60（9 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8VLD Crystal structure of Ash1L PHD finger in complex with histone H3K4me2 Deposited 2024-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 2–12（11 aa）
Chain T 2–12（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6 M sodium citrate pH 6.5
Resolution 1.92 Å R-free 0.249
8VLF Crystal structure of Ash1L PHD finger in complex with histone H3K4me3 Deposited 2024-01-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 2–13（12 aa）
Chain T 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6 M sodium citrate pH 6.5
Resolution 1.34 Å R-free 0.188
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8Z73 Crystal Structure of AF9 in complex with H3K9la peptide Deposited 2024-04-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.4M Sodium Malonate
Resolution 2.91 Å R-free 0.221
8ZXC NMR solution structures of ASH1L BRD-PHD domain in complex with H3K4me2 peptide Deposited 2024-06-14 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–13（12 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) null；Pressure 1
NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 100% D2O | 100% D2O
Resolution not provided
9C0O Crystal structure of DmCfp1 PHD finger bound to H3K4me3 Deposited 2024-05-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–16（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) DMS DIMETHYL SULFOXIDE × 1 ZN ZINC ION × 3 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；15% PEG3350, 0.01M Tris pH8.5, 0.2M Ammonium sulfate
Resolution 1.53 Å R-free 0.194
9DZN KAT6A MYST domain complexed with a H3K14-CoA bisubstrate inhibitor Deposited 2024-10-16 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 6–24（19 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；294.15 K；1.25 M NH4SO4, 0.28 M NaCl, and 0.1 M HEPES pH 6.4
Resolution 1.72 Å R-free 0.245
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315
9IM4 Crystal Structure of AF9 YEATS domain F28R mutant in complex with histone H3K9la Deposited 2024-07-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 2–11（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；2.1M DL Malic acid pH7.0
Resolution 2.79 Å R-free 0.315
9N61 Transporter associated with antigen processing (TAP) bound to the 9-mer peptide RRYQKSTEL and ATP Deposited 2025-02-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 52–60（9 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 6.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9V5M The crystal structure of RBBP4-H3 complex Deposited 2025-05-26 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 2–15（14 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å R-free 0.211

22 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name H3C_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–15； UniProt 12–26

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 21hj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 21hj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id21hj
Deposition date deposition_date2025-12-12
最后修订 last_revision2026-03-11
Structure title titleSolution structures of BRD9 bromodomain in complex with histone H3 lactyl-lysine 18 (H3K18la) peptide
Keywords keywords;histone lactylation, BRD9, chromatin remodeling, chromatin accessibility, transcription regulation, hepatocellular carcinoma, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.08 Å
Radius of gyration Rg (electron density) rg_electron16.60 Å
Forward intensity I(0) i01173550000.00
Molecular weight molecular_weight298870.0 kDa
Excluded volume excluded_volume377590 ų
Envelope volume envelope_volume48556 ų
Hydration-shell volume shell_volume19658 ų
Envelope diameter envelope_diameter76.1 Å
Shell Rg shell_rg27.49 Å
Envelope Rg envelope_rg21.98 Å
Shape Rg shape_rg16.59 Å
Total Rg total_rg16.87 Å
Total atoms total_atoms42200
Residues n_residues2620
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 dmax69.0 Å
Rg (real space) rg_real17.21 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real1.1740e+09
I(0) uncertainty (real space) i0_real_error1.4470e+07
Rg (reciprocal space) rg_reciprocal17.20 Å
I(0) (reciprocal space) i0_reciprocal1174000000.0000
Solution quality estimate total_estimate0.6493
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.2 Å
Skewness Skewness skewness0.606
Kurtosis Kurtosis kurtosis0.216
Angular range angular_range— – 0.4650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha655000.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.336; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.430; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)