SMTL ID : 7la9.1 (2 other biounits)

Crystal structure of the first bromodomain (BD1) of human BRD4 (BRD4-1) in complex with bivalent inhibitor NC-III-49-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x XR7: N,N'-(oxybis{(ethane-2,1-diyl)oxyethane-2,1-diyloxy[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)-4,1-phenylene]})di(ethane-1-sulfonamide)(Non-covalent)

XR7.1: 27 residues within 4Å: Chain A: W.38, P.39, F.40, Q.42, P.43, V.44, D.45, K.48, L.49, L.51, C.93, N.97, I.103 Chain B: W.38, P.39, F.40, Q.42, P.43, V.44, D.45, K.48, L.49, L.51, C.93, N.97, I.103 Ligands: EDO.3 24 PLIP interactions: 12 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:W.38, A:W.38, A:D.45, A:K.48, A:L.51, A:I.103, A:I.103, B:W.38, B:W.38, B:D.45, B:K.48, B:L.49, B:L.51, B:I.103, B:I.103 Hydrogen bonds: A:Q.42, A:D.45, A:N.97, B:Q.42, B:D.45, B:N.97 Water bridges: A:Q.42, A:D.45, B:Q.42

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

EDO.2: 2 residues within 4Å: Chain A: N.87, E.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.87 Water bridges: A:N.87 EDO.3: 2 residues within 4Å: Chain A: W.38 Ligands: XR7.1 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: K.33, H.34, Q.35 Chain B: V.47, K.48 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: V.47, K.48, N.50 Chain B: K.33, H.34, Q.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.50 EDO.6: 2 residues within 4Å: Chain A: W.32 Chain B: K.48 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.48, B:K.48 EDO.10: 5 residues within 4Å: Chain B: I.57, I.58, K.59, T.60, N.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.59, B:T.60, B:N.92, B:N.92 EDO.11: 4 residues within 4Å: Chain B: Q.19, N.78, A.79, Q.80 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.78, B:A.79, B:Q.80

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

CL.7: 1 residues within 4Å: Chain A: W.32 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: H.34 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain B: W.32 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: H.34 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 2 residues within 4Å: Chain B: K.68, E.72 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.68, B:E.72

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
D

Bromodomain-containing protein 4

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