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SMTL ID : 8p9f.1

Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB161

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x X9O: ~{N}-(2-aminophenyl)-4-[2-(2-azanyl-5-methyl-4-oxidanyl-phenyl)hydrazinyl]benzamide(Non-covalent)

X9O.1:

9 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, N.99, I.105

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:F.42, A:V.46, A:L.51, A:L.53, A:I.105, A:I.105
Hydrogen bonds: A:P.41, A:N.99
pi-Stacking: A:W.40

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

EDO.2:	4 residues within 4Å: Chain A: T.62, M.64, R.72, D.87 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.72, A:R.72, A:D.87 Water bridges: A:D.87
EDO.3:	4 residues within 4Å: Chain A: I.85, N.89, F.116, L.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.89
EDO.4:	2 residues within 4Å: Chain A: W.34, Q.43 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.43
EDO.5:	4 residues within 4Å: Chain A: P.45, G.67, T.68, K.71 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.43
EDO.6:	5 residues within 4Å: Chain A: Q.18, L.22, Q.23, L.26, L.73 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.18, A:L.22 Water bridges: A:E.74, A:N.76, A:N.76, A:N.76

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Bauer, N. et al., Development of Potent Dual BET/HDAC Inhibitors via Pharmacophore Merging and Structure-Guided Optimization. Acs Chem.Biol. (2024)

Release Date

2023-07-05

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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