6uvj.1 | SWISS-MODEL Template Library

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SMTL ID : 6uvj.1

Cocrystal of BRD4(D1) with a methyl carbamate thiazepane inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

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

EDO.1:	5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62
EDO.2:	5 residues within 4Å: Chain A: P.101, G.102, V.106, E.110 Ligands: EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.102, A:E.110
EDO.3:	6 residues within 4Å: Chain A: Y.96, N.99, K.100, P.101, V.106 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.99

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4:

3 residues within 4Å:

Chain A: G.102, D.103, D.104

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:D.104
Water bridges: A:I.105
Salt bridges: A:D.103, A:D.104

1 x QJ1: methyl (7S)-7-(thiophen-2-yl)-1,4-thiazepane-4-carboxylate(Non-covalent)

QJ1.5:

9 residues within 4Å:

Chain A: W.40, P.41, F.42, V.46, L.51, L.53, Y.98, N.99, I.105

2 PLIP interactions:

2 interactions with chain A

Hydrophobic interactions: A:I.105
Hydrogen bonds: A:N.99

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Johnson, J.A. et al., Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains. Acs Med.Chem.Lett. (2019)

Release Date

2020-01-01

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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