SMTL ID : 7ogy.1

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-benzyl-N5-cyclopropyl-N3-methyl-1H-pyrazole-3,5-dicarboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Q.103, D.104, E.107, F.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.104 EDO.2: 3 residues within 4Å: Chain A: K.62, D.67, E.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.62, A:K.62, A:E.73 EDO.3: 5 residues within 4Å: Chain A: K.87, Y.88, N.89, P.90, P.91 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: D.45, Y.88 Ligands: VE5.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.45

1 x VE5: N5-cyclopropyl-N3-methyl-1-(phenylmethyl)pyrazole-3,5-dicarboxamide(Non-covalent)

VE5.4: 13 residues within 4Å: Chain A: W.30, P.31, F.32, V.36, L.43, C.85, Y.88, N.89, P.90, H.93, V.95, M.98 Ligands: EDO.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.30, A:L.43, A:L.43, A:Y.88, A:V.95, A:V.95 Hydrogen bonds: A:N.89, A:N.89 Water bridges: A:P.31

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

PEG.6: 5 residues within 4Å: Chain A: L.10, K.11, N.14, M.63, E.64 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.11 Water bridges: A:S.7, A:K.11, A:N.14, A:K.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seal, J.T. et al., Fragment-based Scaffold Hopping: Identification of Potent, Selective, and Highly Soluble Bromo and Extra Terminal Domain (BET) Second Bromodomain (BD2) Inhibitors. J.Med.Chem. (2021)

Release Date

2021-07-28

Peptides

Bromodomain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Bromodomain-containing protein 2

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