SMTL ID : 6uve.1 (1 other biounit)

Crystal structure of BCL-XL bound to compound 7: (R)-3-(Benzylthio)-2-(3-(4-chloro-[1,1':2',1'':3'',1'''-quaterphenyl]-4'''-carbonyl)-3-(4-methylbenzyl)ureido)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-dimer

Ligands

2 x QHV: (R)-3-(Benzylthio)-2-(3-(4-chloro-[1,1':2',1'':3'',1'''-quaterphenyl]-4'''-carbonyl)-3-(4-methylbenzyl)ureido)propanoic acid(Non-covalent)

QHV.1: 18 residues within 4Å: Chain A: A.42, E.45, F.46, Y.50, A.53, V.75, L.79, N.85, W.86, G.87, R.88, V.90, A.91, S.94, F.95, A.98, F.140, Y.144 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.42, A:F.46, A:F.46, A:F.46, A:F.46, A:F.46, A:Y.50, A:A.53, A:L.79, A:L.79, A:W.86, A:V.90, A:A.91, A:F.95, A:F.140, A:Y.144, A:Y.144 pi-Stacking: A:F.95 pi-Cation interactions: A:R.88 QHV.3: 18 residues within 4Å: Chain B: A.42, E.45, F.46, R.49, Y.50, F.54, V.75, L.79, N.85, W.86, G.87, R.88, V.90, A.91, S.94, F.95, F.140, Y.144 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.46, B:F.46, B:F.46, B:F.46, B:Y.50, B:Y.50, B:F.54, B:F.54, B:L.79, B:L.79, B:W.86, B:R.88, B:V.90, B:A.91, B:F.95, B:F.95, B:F.140, B:Y.144, B:Y.144 Hydrogen bonds: B:N.85 pi-Cation interactions: B:R.88

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

EDO.2: 1 residues within 4Å: Chain A: N.134 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roy, M.J. et al., Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-X L and BCL-2. J.Med.Chem. (2021)

Release Date

2021-05-05

Peptides

Bcl-2-like protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bcl-2-like protein 1

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