SMTL ID : 5s9o.1 (1 other biounit)

CRYSTAL STRUCTURE OF THE HUMAN BRD2 BD1 BROMODOMAIN IN COMPLEX WITH 9-(cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3-(3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 Å

Oligo State

monomer

Ligands

1 x YW1: 9-(cyclopropylmethyl)-7-[(2R,6S)-2,6-dimethylmorpholine-4-carbonyl]-3-(3,5-dimethyl-1,2-oxazol-4-yl)-9H-carbazole-1-carboxamide(Non-covalent)

YW1.1: 14 residues within 4Å: Chain A: W.47, P.48, F.49, Q.51, P.52, V.53, D.54, K.57, L.58, L.60, C.102, N.106, I.112 Ligands: EDO.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.47, A:W.47, A:P.48, A:F.49, A:L.58, A:I.112, A:I.112 Hydrogen bonds: A:P.48, A:D.54, A:N.106 Water bridges: A:C.102 pi-Stacking: A:W.47, A:W.47

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

EDO.2: 5 residues within 4Å: Chain A: D.110, D.111, I.112 Ligands: YW1.1, EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.111, A:I.112 EDO.3: 4 residues within 4Å: Chain A: T.109, D.110, D.111 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.111 Water bridges: A:D.111 EDO.4: 2 residues within 4Å: Chain A: R.24, E.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.24, A:R.24 Water bridges: A:E.136 EDO.5: 4 residues within 4Å: Chain A: Y.105, N.106, K.107, D.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.106, A:K.107 EDO.6: 3 residues within 4Å: Chain A: S.89, M.92, Q.93 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.89, A:S.89 EDO.7: 5 residues within 4Å: Chain A: I.66, I.67, K.68, Q.69, N.101 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.66, A:K.68, A:Q.69, A:Q.69, A:N.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavai, A.V. et al., Discovery and Preclinical Pharmacology of an Oral Bromodomain and Extra-Terminal (BET) Inhibitor Using Scaffold-Hopping and Structure-Guided Drug Design. J.Med.Chem. (2021)

Release Date

2021-09-29

Peptides

Bromodomain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 2

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