SMTL ID : 6cj1.1

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor JWG071

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

1 x F2S: 11-[(2R)-butan-2-yl]-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one(Non-covalent)

F2S.1: 11 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, Y.98, N.99, I.105 Ligands: FND.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.40, A:L.51, A:L.53, A:Y.98, A:Y.98, A:I.105 Hydrogen bonds: A:N.99 Water bridges: A:Q.44, A:Q.44 pi-Stacking: A:W.40

1 x FND: 11-[(2S)-butan-2-yl]-2-({2-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one(Non-covalent)

FND.2: 11 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, L.53, Y.98, N.99, I.105 Ligands: F2S.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.40, A:W.40, A:P.41, A:L.51, A:L.53, A:Y.98, A:Y.98, A:I.105, A:I.105 Hydrogen bonds: A:N.99 Water bridges: A:Q.44, A:Q.44 pi-Stacking: A:W.40

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

EDO.3: 2 residues within 4Å: Chain A: D.103, D.104 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.103, A:D.104, A:D.104 Water bridges: A:D.103, A:D.103, A:I.105 EDO.4: 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.5: 1 residues within 4Å: Chain A: N.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.11 Water bridges: A:N.13

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 6 residues within 4Å: Chain A: R.17, T.19, Q.21, L.22, N.80, A.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.81 Water bridges: A:Q.21 NO3.7: 4 residues within 4Å: Chain A: Q.37, F.38, W.40, M.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.37, A:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. ACS Chem. Biol. (2018)

Release Date

2018-08-29

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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