SMTL ID : 7mr5.1

Crystal structure of the first bromodomain (BD1) of human BRD4 bound to GXH-II-052

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

1 x ZMS: N,N'-{oxybis[(ethane-2,1-diyl)oxy(1-oxoethane-2,1-diyl)piperidine-1,4-diyl]}bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide}(Non-covalent)

ZMS.1: 29 residues within 4Å: Chain A: Q.37, F.38, W.40, P.41, F.42, V.46, L.51, L.53, Y.98, N.99, D.104, I.105, M.108 Chain B: W.40, P.41, F.42, Q.44, P.45, V.46, D.47, V.49, K.50, L.51, N.52, L.53, Y.98, N.99, I.105 Ligands: EDO.3 26 PLIP interactions: 14 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:P.41, B:F.42, B:Q.44, B:V.46, B:L.51, B:L.53, B:Y.98, A:Q.37, A:F.38, A:W.40, A:W.40, A:P.41, A:F.42, A:V.46, A:L.51, A:L.53 Hydrogen bonds: B:P.41, B:D.47, B:K.50, B:N.52, B:N.99, B:N.99, A:P.41, A:N.99, A:N.99 Water bridges: B:Y.56

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

EDO.2: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 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.3: 4 residues within 4Å: Chain A: D.103, D.104, I.105 Ligands: ZMS.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.105 Water bridges: A:D.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guan, X. et al., Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity. J.Med.Chem. (2022)

Release Date

2022-05-18

Peptides

Bromodomain-containing protein 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bromodomain-containing protein 4

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