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SMTL ID : 6dml.1

A multiconformer ligand model of 3,5 dimethylisoxaxole bound to the bromodomain of human BRD4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

EDO.1:	4 residues within 4Å: Chain A: Q.44, P.45, K.71 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.45
EDO.2:	5 residues within 4Å: Chain A: Q.18, T.19, N.20, Q.23, E.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.23, A:Q.23
EDO.3:	10 residues within 4Å: Chain A: P.6, T.9, Q.43, Q.44, P.45, D.65, G.67, T.68, K.71 Ligands: EDO.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.71

1 x 9BM: 4-((2-(tert-butyl)phenyl)amino)-7-(3,5-dimethylisoxazol-4-yl)-6-methoxy-1,5-naphthyridine-3-carboxylic acid(Non-covalent)

9BM.4:

14 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, Y.56, C.95, Y.98, N.99, D.104, I.105, M.108

10 PLIP interactions:

10 interactions with chain A

Hydrophobic interactions: A:W.40, A:W.40, A:P.41, A:F.42, A:L.51, A:L.53, A:Y.98
Hydrogen bonds: A:N.99
Water bridges: A:Q.44, A:C.95

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

van Zundert, G.C.P. et al., qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. (2018)

Release Date

2018-12-19

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Bromodomain-containing protein 4

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