SMTL ID : 5cy9.1

Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: Q.58, P.59, V.60, D.61, L.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58, A:D.61

1 x E0A: N-(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)butane-1-sulfonamide(Non-covalent)

E0A.2: 10 residues within 4Å: Chain A: W.54, P.55, F.56, V.60, L.65, L.67, N.113, D.118, I.119, M.122 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.55, A:F.56, A:V.60, A:L.65, A:L.67, A:L.67, A:D.118, A:I.119 Hydrogen bonds: A:N.113

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

EDO.3: 5 residues within 4Å: Chain A: R.14, A.62, L.67, D.69, Y.70 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.14, A:D.69, A:Y.70 Water bridges: A:Y.71 EDO.4: 5 residues within 4Å: Chain A: S.24, N.25, P.26, K.30, N.89 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.25, A:K.30 Water bridges: A:K.28 EDO.5: 3 residues within 4Å: Chain A: W.48, K.49, K.84 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xue, X. et al., Discovery of Benzo[cd]indol-2(1H)-ones as Potent and Specific BET Bromodomain Inhibitors: Structure-Based Virtual Screening, Optimization, and Biological Evaluation. J.Med.Chem. (2016)

Release Date

2016-01-13

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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