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SMTL ID : 4ioo.1

Crystal Structure of the first bromodomain of BRD4 in complex with N-methyltrimethylacetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

EDO.1:	6 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94, I.97 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62
EDO.2:	3 residues within 4Å: Chain A: Q.118, K.119, E.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.119, A:E.122, A:E.122 Water bridges: A:K.119
EDO.3:	6 residues within 4Å: Chain A: R.17, Q.18, L.22, Q.23, L.73, N.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.76 Water bridges: A:N.76
EDO.4:	2 residues within 4Å: Chain A: N.89, T.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.93 Water bridges: A:T.93
EDO.5:	5 residues within 4Å: Chain A: W.40, P.41, I.105, M.108 Ligands: BAE.6 No protein-ligand interaction detected (PLIP)

1 x BAE: N-methyltrimethylacetamide(Non-covalent)

BAE.6:

10 residues within 4Å:

Chain A: P.41, F.42, V.46, L.51, L.53, Y.98, N.99, I.105
Ligands: EDO.5, DMS.7

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:L.51, A:Y.98, A:I.105
Hydrogen bonds: A:N.99
Water bridges: A:P.41

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

DMS.7:

7 residues within 4Å:

Chain A: P.41, V.46, L.53, C.95, N.99, I.105
Ligands: BAE.6

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:N.99

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Lolli, G. et al., Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-10-02

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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