8p9k.1 | SWISS-MODEL Template Library

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SMTL ID : 8p9k.1

Crystal structure of the first bromodomain of human BRD4 in complex with the dual BET/HDAC inhibitor NB503

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

EDO.1:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
EDO.3:	2 residues within 4Å: Chain A: W.34, Q.43 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.43
EDO.4:	6 residues within 4Å: Chain A: K.14, R.17, L.22, N.76, Y.78, W.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.14, A:R.17, A:N.76, A:Y.78
EDO.5:	6 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, 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.6:	5 residues within 4Å: Chain A: P.7, 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.7:	2 residues within 4Å: Chain A: V.49, K.50 No protein-ligand interaction detected (PLIP)

1 x X9U: ~{N}-(2-azanyl-5-phenyl-phenyl)-4-(6-methyl-7-oxidanylidene-1~{H}-pyrrolo[2,3-c]pyridin-4-yl)benzamide(Non-covalent)

X9U.2:

8 residues within 4Å:

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

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:W.40, A:P.41, A:L.51, A:L.51, A:I.105
Hydrogen bonds: A:N.99, A:N.99
Water bridges: A:Q.44
pi-Stacking: A:W.40

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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