SMTL ID : 8wyg.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor 22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

homo-tetramer

Ligands

4 x XHN: 2-[[5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-2-oxidanylidene-pyridin-4-yl]amino]-~{N}-(4-oxidanylcyclohexyl)ethanamide(Non-covalent)

XHN.1: 17 residues within 4Å: Chain A: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, V.116, M.119 Chain C: A.48, W.51, M.119 Ligands: XHN.3 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.51, A:W.51, A:W.51, A:P.52, A:D.58, A:V.116 Hydrogen bonds: A:D.58, A:N.110 pi-Stacking: A:H.114, C:W.51, C:W.51 XHN.2: 14 residues within 4Å: Chain B: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, D.115, V.116, M.119 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.51, B:P.52, B:D.58, B:L.62, B:V.116, B:V.116 Hydrogen bonds: B:D.58, B:N.110 pi-Stacking: B:H.114 XHN.3: 19 residues within 4Å: Chain A: A.48, W.51, D.115, M.119 Chain C: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, D.115, V.116, M.119 Ligands: XHN.1 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain C pi-Stacking: A:W.51, A:W.51, C:H.114 Halogen bonds: A:D.115 Hydrophobic interactions: C:W.51, C:P.52, C:D.58, C:L.62, C:L.64 Hydrogen bonds: C:D.58, C:N.110 XHN.4: 14 residues within 4Å: Chain D: W.51, P.52, F.53, P.56, V.57, D.58, L.62, L.64, C.106, N.110, H.114, D.115, V.116, M.119 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.51, D:W.51, D:W.51, D:P.52, D:D.58, D:L.62, D:L.62 Hydrogen bonds: D:D.58, D:N.110 pi-Stacking: D:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, W. et al., Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia. J.Med.Chem. (2024)

Release Date

2024-01-24

Peptides

Bromodomain-containing protein 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bromodomain-containing protein 2

Related Entries With Identical Sequence