SMTL ID : 9kla.1

Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22024

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

4 x 01: 1-[1-(3,5-dimethoxyphenyl)indolizin-3-yl]ethanone

01.1: 8 residues within 4Å: Chain A: H.48, G.49, F.50, F.51, V.55, I.59, N.106, Y.112 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.51, A:V.55, A:I.59, A:I.59, A:Y.112 Hydrogen bonds: A:N.106 pi-Stacking: A:F.50, A:Y.112, A:Y.112 01.4: 7 residues within 4Å: Chain A: H.37, L.135, M.139 Chain B: S.138, M.139 Ligands: MLT.3, 01.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.135 01.5: 8 residues within 4Å: Chain B: H.48, G.49, F.50, F.51, V.55, I.59, N.106, Y.112 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.51, B:V.55, B:I.59, B:I.59, B:Y.112 Hydrogen bonds: B:N.106 pi-Stacking: B:F.50, B:Y.112, B:Y.112 01.8: 7 residues within 4Å: Chain A: S.138, M.139 Chain B: H.37, L.135, M.139 Ligands: 01.4, MLT.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.135

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: F.15, G.18, S.19, L.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18, A:L.20 GOL.6: 4 residues within 4Å: Chain B: F.15, G.18, S.19, L.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.18, B:L.20

2 x MLT: D-MALATE(Non-covalent)

MLT.3: 4 residues within 4Å: Chain A: H.37, F.38, R.131 Ligands: 01.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.38 Salt bridges: A:H.37, A:H.37, A:R.131 MLT.7: 4 residues within 4Å: Chain B: H.37, F.38, R.131 Ligands: 01.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.38 Salt bridges: B:H.37, B:H.37, B:R.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Z. et al., Key imidazolyl groups that induce phenylalanine flipping enhance the efficacy of oral BRD9 inhibitors for AML treatment. Acta Pharm Sin B (2025)

Release Date

2025-11-05

Peptides

Bromodomain-containing protein 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bromodomain-containing protein 9

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