SMTL ID : 7wni.1

Crystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor Y13158

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.12 Å

Oligo State

homo-dimer

Ligands

2 x JGU: 7-[2-[2,4-bis(fluoranyl)phenoxy]-5-(2-oxidanylpropan-2-yl)phenyl]-2-[4-(2-hydroxyethyloxy)-3,5-dimethyl-phenyl]-5-methyl-furo[3,2-c]pyridin-4-one(Non-covalent)

JGU.1: 14 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, D.115, V.116, M.119 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.51, A:D.58, A:L.62, A:L.62 Hydrogen bonds: A:D.58, A:N.110 JGU.6: 13 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, D.115, V.116, M.119 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.51, B:D.58, B:L.62, B:L.64, B:L.64 Hydrogen bonds: B:P.56, B:D.58, B:N.110 pi-Stacking: B:W.51

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

EDO.2: 4 residues within 4Å: Chain A: E.40, H.46, V.126, R.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.46, A:R.130 EDO.3: 3 residues within 4Å: Chain A: H.114, D.115 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.114, A:D.115 EDO.4: 5 residues within 4Å: Chain A: H.114, D.115, V.116 Ligands: JGU.1, EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.115, A:V.116 EDO.7: 3 residues within 4Å: Chain A: P.112, R.121 Chain B: F.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.121

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 9 residues within 4Å: Chain A: Y.107, N.110, P.111, P.112, V.117, R.121 Chain B: D.125, E.128, F.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.107, A:N.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structure-Based Discovery and Optimization of Furo[3,2- c ]pyridin-4(5 H )-one Derivatives as Potent and Second Bromodomain (BD2)-Selective Bromo and Extra Terminal Domain (BET) Inhibitors. J.Med.Chem. (2022)

Release Date

2022-08-10

Peptides

Isoform 4 of Bromodomain-containing protein 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 4 of Bromodomain-containing protein 2

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