SMTL ID : 6kek.1

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6-hydroxy-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 5 residues within 4Å: Chain A: I.59, I.60, K.61, T.62, N.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.61, A:T.62 FMT.2: 3 residues within 4Å: Chain A: N.3, V.46, D.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47 FMT.3: 7 residues within 4Å: Chain A: R.17, L.22, R.72, L.73, N.76, Y.77, Y.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.78 FMT.4: 1 residues within 4Å: Ligands: D7L.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.44 FMT.5: 5 residues within 4Å: Chain A: T.19, Q.21, N.80, A.81 Ligands: FMT.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.17, A:A.81 FMT.6: 3 residues within 4Å: Chain A: Y.57, K.58, K.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.61 FMT.7: 4 residues within 4Å: Chain A: T.19, N.20, Q.21 Ligands: FMT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:N.20, A:Q.21

1 x D7L: 6-hydroxy-16-methoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(16),3,5,7,9,13(17),14-heptaen-12-one(Non-covalent)

D7L.8: 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: FMT.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.41, A:L.51, A:L.51, A:Y.98, A:I.105, A:I.105 Hydrogen bonds: A:N.99 pi-Stacking: A:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoo, M. et al., Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research. Molecules (2021)

Release Date

2020-07-08

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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