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 17–123 | Fragment：bromodomain (UNP residues 17-123) | 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 |
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 4YY4 | 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 |
| 4YY6 Crystal structure of BRD9 Bromodomain bound to a butyryllysine peptide Deposited 2015-03-23 | 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 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 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 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 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 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 | 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 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 |
| 4Z6I Crystal structure of BRD9 bromodomain in complex with a substituted valerolactam quinolone ligand Deposited 2015-04-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
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 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 | 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 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 73 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 2–108； UniProt 17–123 |
