SMTL ID : 5d0c.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 1.49 Å

Oligo State

monomer

Ligands

3 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 4 residues within 4Å: Chain A: D.117, D.118, I.119 Ligands: E0B.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.118, A:I.119 Water bridges: A:D.117 NO3.2: 9 residues within 4Å: Chain A: G.15, S.16, A.62, L.67, P.68, D.69, Y.70, Y.71, K.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.16, A:S.16, A:Y.71, A:K.72 NO3.3: 5 residues within 4Å: Chain A: T.33, Q.35, L.36, N.94, A.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.33, A:L.36, A:A.95 Water bridges: A:Q.96

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

EDO.4: 5 residues within 4Å: Chain A: P.59, D.79, G.81, T.82, K.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.81, A:T.82 EDO.5: 5 residues within 4Å: Chain A: W.54, P.55, Q.58, L.65 Ligands: E0B.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.58, A:Q.58

1 x E0B: N-[(1-acetylpiperidin-4-yl)methyl]-1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide(Non-covalent)

E0B.6: 11 residues within 4Å: Chain A: W.54, P.55, F.56, V.60, L.65, L.67, Y.70, N.113, M.122 Ligands: NO3.1, EDO.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.54, A:P.55, A:F.56, A:L.65, A:L.67, A:L.67 Hydrogen bonds: A:N.113

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 2 residues within 4Å: Chain A: K.75, P.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.75

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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