SMTL ID : 7oet.1

C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1,5-dimethyl-N-(2-(methylamino)-2-oxo-1-(tetrahydro-2H-pyran-4-yl)ethyl)-6-oxo-N-(2-phenyl-2-(pyridin-2-yl)ethyl)-1,6-dihydropyridine-3-carboxamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x 80Z: 1,5-dimethyl-~{N}-[(1~{R})-2-(methylamino)-1-(oxan-4-yl)-2-oxidanylidene-ethyl]-6-oxidanylidene-~{N}-[(2~{S})-2-phenyl-2-pyridin-2-yl-ethyl]pyridine-3-carboxamide(Non-covalent)

80Z.1: 12 residues within 4Å: Chain A: W.30, P.31, F.32, K.34, V.36, L.41, L.43, Y.88, N.89, H.93, V.95, M.98 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.30, A:W.30, A:P.31, A:F.32, A:V.36, A:L.41, A:V.95, A:V.95 Hydrogen bonds: A:N.89 Water bridges: A:D.37, A:D.37 pi-Cation interactions: A:H.93

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

EDO.2: 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.3: 2 residues within 4Å: Chain A: K.62, D.67 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.62, A:K.62, A:D.77 EDO.4: 4 residues within 4Å: Chain A: K.87, Y.88, N.89, P.90 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.89

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.5: 6 residues within 4Å: Chain A: S.7, L.10, K.11, N.14, E.64, R.66 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.66 Hydrogen bonds: A:K.11, A:N.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rianjongdee, F. et al., Discovery of a Highly Selective BET BD2 Inhibitor from a DNA-Encoded Library Technology Screening Hit. J.Med.Chem. (2021)

Release Date

2021-10-13

Peptides

Bromodomain-containing protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Bromodomain-containing protein 2

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