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SMTL ID : 5kj0.1

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH DB-1-264-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

1 x 6TB: 4-[[(7~{R})-8-cyclopentyl-7-ethyl-5-methyl-6-oxidanylidene-7~{H}-pteridin-2-yl]-methyl-amino]-3-methoxy-~{N}-(1-methylpiperidin-4-yl)benzamide(Non-covalent)

6TB.1:

14 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, D.47, K.50, L.51, L.53, Y.56, C.95, Y.98, N.99, I.105

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:W.40, A:V.46, A:L.51, A:L.53, A:Y.56, A:Y.98
Hydrogen bonds: A:Q.44, A:N.99
Water bridges: A:D.47

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

EDO.2:	7 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, T.90, N.94, I.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62, A:N.94
EDO.3:	4 residues within 4Å: Chain A: G.102, V.106, L.107, E.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.102 Water bridges: A:E.110
EDO.4:	4 residues within 4Å: Chain A: Y.24, Q.118, K.119, E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.119, A:E.122
EDO.5:	6 residues within 4Å: Chain A: I.85, N.89, F.116, L.117, I.120 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.89
EDO.6:	1 residues within 4Å: Chain A: K.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.58
EDO.7:	4 residues within 4Å: Chain A: N.89, T.93, E.113 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.93, A:T.93 Water bridges: A:Q.86, A:E.113
EDO.8:	8 residues within 4Å: Chain A: R.17, Q.18, L.22, Q.23, L.26, L.73, N.76, Y.78 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.76

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Koblan, L.W. et al., Assessment of Bromodomain Target Engagement by a Series of BI2536 Analogues with Miniaturized BET-BRET. ChemMedChem (2016)

Release Date

2017-08-09

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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