SMTL ID : 7l9m.1

Crystal structure of the first bromodomain (BD1) of human BRD4 in complex with bivalent inhibitor GXH-II-083

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 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 EDO.2: 5 residues within 4Å: Chain A: D.104, L.107 Chain B: W.40, Q.43 Ligands: XR4.4 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.43, A:D.104 Water bridges: B:W.34, B:Q.43 EDO.3: 7 residues within 4Å: Chain A: S.1, M.2, N.3, A.48, L.53, P.54, Y.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.1, A:N.3 EDO.5: 6 residues within 4Å: Chain B: I.59, I.60, K.61, T.62, N.94, I.97 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.59, B:K.61, B:T.62, B:T.62, B:T.62, B:N.94

1 x XR4: N,N'-[(1,19-dioxo-4,7,10,13,16-pentaoxanonadecane-1,19-diyl)di(piperidine-1,4-diyl)]bis(4-{[4-({3-[(tert-butylsulfonyl)amino]-4-chlorophenyl}amino)-5-methylpyrimidin-2-yl]amino}-2-fluorobenzamide)(Non-covalent)

XR4.4: 29 residues within 4Å: Chain A: Q.37, F.38, W.40, P.41, F.42, V.46, K.50, L.51, L.53, 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.2 28 PLIP interactions: 15 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:F.42, B:Q.44, B:V.46, B:L.53, B:L.53, B:Y.98, A:Q.37, A:F.38, 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:K.50, A:N.99, A:N.99, A:D.104 Water bridges: B:Y.56, B:Y.98 pi-Stacking: B:W.40

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

2022-01-12

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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