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SMTL ID : 7r9c.1

Cocrystal of BRD4(D1) with N,N-dimethyl-2-[(3R)-3-(5-{2-[2-methyl-5-(propan-2-yl)phenoxy]pyrimidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-1-yl)pyrrolidin-1-yl]ethan-1-amine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

EDO.1:	4 residues within 4Å: Chain A: Y.96, V.106, E.110, E.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.110
EDO.3:	8 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, T.90, T.93, 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.4:	5 residues within 4Å: Chain A: N.3, P.45, V.46, D.47, K.50 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.3
EDO.5:	8 residues within 4Å: Chain A: W.34, K.35, H.36, Q.37, A.39, W.40, Q.43 Ligands: CL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.34
EDO.6:	3 residues within 4Å: Chain A: N.20, Q.21, P.124 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.20

1 x 2IR: N,N-dimethyl-2-[(3R)-3-(5-{2-[2-methyl-5-(propan-2-yl)phenoxy]pyrimidin-4-yl}-4-[4-(trifluoromethyl)phenyl]-1H-imidazol-1-yl)pyrrolidin-1-yl]ethan-1-amine(Non-covalent)

2IR.2:

16 residues within 4Å:

Chain A: P.41, F.42, Q.44, V.46, L.51, L.53, Y.56, M.64, D.65, M.91, N.94, C.95, Y.98, N.99, D.103, I.105

7 PLIP interactions:

7 interactions with chain A

Hydrophobic interactions: A:F.42, A:V.46, A:L.51, A:Y.56, A:I.105
Hydrogen bonds: A:N.99
Salt bridges: A:D.103

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7:

3 residues within 4Å:

Chain A: W.34, Q.43
Ligands: EDO.5

Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Cui, H. et al., A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J.Med.Chem. (2022)

Release Date

2022-01-19

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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