SMTL ID : 6uvg.3 (5 other biounits)

Crystal structure of BCL-XL bound to compound 13: (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-(((3R,5R,7R)-adamantan-1-ylmethyl)sulfonyl)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x QHP: (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-(((3R,5R,7R)-adamantan-1-ylmethyl)sulfonyl)propanoic acid(Non-covalent)

QHP.1: 16 residues within 4Å: Chain A: A.42, E.45, F.46, R.49, Y.50, A.53, F.54, L.57, L.79, N.85, W.86, G.87, R.88, A.91, L.143, Y.144 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.42, A:F.46, A:F.46, A:Y.50, A:A.53, A:L.57, A:L.57, A:L.79, A:W.86, A:R.88, A:A.91, A:Y.144 Hydrogen bonds: A:N.85 Water bridges: A:R.88, A:R.88 Salt bridges: A:R.88 pi-Stacking: A:F.46, A:Y.50 QHP.3: 16 residues within 4Å: Chain B: A.42, E.45, F.46, Y.50, A.53, F.54, L.57, L.79, N.85, W.86, G.87, R.88, A.91, F.140, L.143, Y.144 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:E.45, B:F.46, B:F.46, B:F.46, B:A.53, B:L.57, B:L.57, B:L.79, B:W.86, B:A.91, B:F.140, B:L.143, B:Y.144, B:Y.144 Hydrogen bonds: B:N.85 pi-Stacking: B:F.46, B:Y.50

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

EDO.2: 3 residues within 4Å: Chain A: S.30, Q.31, M.32 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.30, A:Q.31, A:M.32 Water bridges: A:S.30

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
E

B
F

Bcl-2-like protein 1

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