SMTL ID : 5cs8.1

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 1.62 Å

Oligo State

monomer

Ligands

1 x EB8: methyl 2-[(1-ethyl-2-oxo-1,2-dihydrobenzo[cd]indol-6-yl)sulfamoyl]benzoate(Non-covalent)

EB8.1: 12 residues within 4Å: Chain A: W.54, P.55, F.56, V.60, L.65, L.67, Y.70, Y.112, N.113, D.118, I.119, M.122 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.54, A:P.55, A:P.55, A:F.56, A:L.65, A:L.67, A:L.67, A:Y.112, A:D.118, A:I.119, A:I.119 Hydrogen bonds: A:N.113

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

NO3.2: 3 residues within 4Å: Chain A: K.28, P.29, K.30 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.30, A:K.30, A:K.30 NO3.3: 6 residues within 4Å: Chain A: H.7, H.8, H.9, H.10, L.11, V.12 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.8, A:H.9, A:H.9, A:H.10, A:L.11, A:V.12

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

EDO.4: 5 residues within 4Å: Chain A: I.73, I.74, K.75, T.76, N.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.73, A:K.75, A:T.76, A:T.76 EDO.5: 5 residues within 4Å: Chain A: Q.57, P.59, G.81, T.82, K.85 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: N.27, P.29 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: P.19, P.20, P.21, P.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.19 GOL.8: 2 residues within 4Å: Chain A: R.14, G.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.15 GOL.9: 3 residues within 4Å: Chain A: Y.110, V.120, E.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.124 Water bridges: A:G.116

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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