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SMTL ID : 7lh8.1

CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH INHIBITOR JJ-II-131

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x XZG: (5R)-1-ethyl-5-(4-methylphenyl)-7-({1-[(4-nitrophenyl)methyl]piperidin-4-yl}methyl)-5,7,8,9-tetrahydro-1H-pyrrolo[3',4':5,6]pyrido[2,3-d]pyrimidine-2,4,6(3H)-trione(Non-covalent)

XZG.1:

14 residues within 4Å:

Chain A: W.40, P.41, F.42, V.46, L.51, L.53, Y.56, Y.98, N.99, D.104, I.105, M.108
Ligands: EDO.5, EDO.6

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:F.42, A:D.104, A:I.105
Hydrogen bonds: A:N.99, A:N.99

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

EDO.2:	3 residues within 4Å: Chain A: P.45, G.67, T.68 No protein-ligand interaction detected (PLIP)
EDO.3:	6 residues within 4Å: Chain A: S.10, N.11, 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:N.11, A:Y.77
EDO.4:	3 residues within 4Å: Chain A: R.17, W.79, N.80 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:N.80
EDO.5:	3 residues within 4Å: Chain A: W.40, Q.44 Ligands: XZG.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.44
EDO.6:	3 residues within 4Å: Chain A: K.50, L.51 Ligands: XZG.1 No protein-ligand interaction detected (PLIP)
EDO.7:	5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.59, A:K.61, A:T.62, A:T.62

1 x NA: SODIUM ION(Non-functional Binders)

NA.8:

5 residues within 4Å:

Chain A: R.17, T.19, Q.21, N.80, A.81

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:R.17, A:T.19, A:Q.21, A:A.81

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Jiang, J. et al., Dihydropyridine Lactam Analogs Targeting BET Bromodomains. Chemmedchem (2022)

Release Date

2022-07-06

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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2oss.1 | 2yel.1 | 3mxf.1 | 3p5o.1 | 3svf.1 | 3svg.1 | 3u5j.1 | 3u5k.1 | 3u5k.2 | 3u5k.3 | 3u5k.4 | 3u5l.1 | 3uvw.1 | 3uvx.1 | 3uvy.1 | 3uw9.1 | 3uw9.2 | 3zyu.1 | 3zyu.2 | 4a9l.1 | 4bw1.1 | 4bw2.1 | 4bw3.1 | 4bw4.1 | 4c67.1 | 4cfk.1 | 4cfl.1 | 4cl9.1 | 4clb.1 | 4e96.1 more...less...

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