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SMTL ID : 6g0e.1

BRD4 (BD1) in complex with APSC-derived ligands

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

1 x EGN: 4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one(Non-covalent)

EGN.1:

12 residues within 4Å:

Chain A: P.41, F.42, V.46, L.51, N.52, L.53, P.54, D.55, Y.56, Y.98, N.99, I.105

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:P.41, A:F.42, A:L.51
Hydrogen bonds: A:N.99
Salt bridges: A:D.55

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2:	4 residues within 4Å: Chain A: P.5, P.6, P.7, P.63 No protein-ligand interaction detected (PLIP)
FMT.3:	5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.61, A:T.62, A:N.94

2 x NA: SODIUM ION(Non-functional Binders)

NA.4:	3 residues within 4Å: Chain A: Y.96, I.97, N.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.96
NA.5:	3 residues within 4Å: Chain A: Y.24, K.119, E.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.24, A:Y.24, A:E.122 Water bridges: A:N.121

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6:

2 residues within 4Å:

Chain A: A.48, N.52

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:A.48

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Humbeck, L. et al., Discovery of an Unexpected Similarity in Ligand Binding Between BRD4 and PPARgamma. Chemrxiv (2019)

Release Date

2020-01-08

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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