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SMTL ID : 5kdh.1

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH A DIHYDROPYRIDOPYRIMIDINE SCAFFOLD INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x 6RX: (5~{S})-1-ethyl-5-(4-methylphenyl)-8,9-dihydro-5~{H}-furo[3,4]pyrido[3,5-~{b}]pyrimidine-2,4,6-trione(Non-covalent)

6RX.1:

13 residues within 4Å:

Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, Y.56, C.95, Y.98, N.99, D.104, I.105, M.108

9 PLIP interactions:

9 interactions with chain A

Hydrophobic interactions: A:W.40, A:P.41, A:F.42, A:V.46, A:L.51, A:I.105
Hydrogen bonds: A:N.99, A:N.99
Water bridges: A:P.41

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

EDO.2:

8 residues within 4Å:

Chain A: S.10, N.11, P.12, K.14, K.16, N.75, N.76, Y.77

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:N.11, A:K.16
Water bridges: A:P.12, A:K.14

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3:	2 residues within 4Å: Chain A: K.58, K.61 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.58, A:K.61
SO4.4:	4 residues within 4Å: Chain A: F.38, D.104, L.107, M.108 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ayoub, A.M. et al., BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen. J. Med. Chem. (2017)

Release Date

2017-08-02

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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