SMTL ID : 9km1.1

Crystal Structure of the bromodomain of human BRD9 in complex with the inhibitor Y22077

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-dimer

Ligands

2 x 01: 1-[1-[4-(imidazol-1-ylmethyl)-3,5-dimethoxy-phenyl]indolizin-3-yl]propan-1-one

01.1: 13 residues within 4Å: Chain A: G.49, F.50, F.51, F.53, V.55, I.59, A.60, N.106, Y.112 Chain B: H.48, F.50, V.111 Ligands: EDO.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.50, A:F.51, A:I.59, A:A.60, A:Y.112 Hydrogen bonds: A:N.106 pi-Stacking: A:Y.112, A:Y.112 01.3: 13 residues within 4Å: Chain A: H.48, F.50, Y.112 Chain B: G.49, F.50, F.51, F.53, V.55, I.59, A.60, N.106, Y.112 Ligands: EDO.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.51, B:I.59, B:A.60, B:Y.112 Hydrogen bonds: B:N.106 pi-Stacking: B:Y.112, B:Y.112

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: I.59, Y.112 Chain B: V.111 Ligands: 01.1 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.111, A:Y.112 EDO.4: 4 residues within 4Å: Chain A: T.110, V.111 Chain B: I.59 Ligands: 01.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.111, B:I.59

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
B

Bromodomain-containing protein 9

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