SMTL ID : 6uvf.6 (5 other biounits)

Crystal structure of BCL-XL bound to compound 12: (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl)propanoic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 2 residues within 4Å: Chain A: K.25 Chain B: R.51 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.51, A:K.25 SO4.2: 2 residues within 4Å: Chain A: S.30, M.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.30, A:S.30, A:M.32

2 x QHS: (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl)propanoic acid(Non-covalent)

QHS.3: 19 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, V.90, A.91, F.140, L.143, Y.144, N.147 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.42, A:F.46, A:F.46, A:F.46, A:F.46, A:Y.50, A:Y.50, A:Y.50, A:A.53, A:L.57, A:L.79, A:V.90, A:A.91, A:F.140, A:L.143, A:Y.144, A:Y.144 Hydrogen bonds: A:N.85 QHS.4: 16 residues within 4Å: Chain B: 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, F.140, L.143, Y.144 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.45, 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 Hydrogen bonds: B:N.85 pi-Stacking: B:F.46

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
K

B
L

Bcl-2-like protein 1

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