SMTL ID : 6uvf.5 (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

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

SO4.1: 2 residues within 4Å: Chain A: R.51 Chain B: K.25 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.25, A:R.51 SO4.2: 2 residues within 4Å: Chain A: K.25 Chain B: R.51 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.25, B:R.51 SO4.4: 5 residues within 4Å: Chain A: E.12 Chain B: W.29, S.30, Q.31, M.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.30, B:Q.31

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

QHS.3: 15 residues within 4Å: Chain A: 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, Y.144 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:F.46, A:F.46, A:Y.50, A:A.53, A:L.57, A:L.79, A:R.88, A:A.91, A:F.140, A:Y.144 Hydrogen bonds: A:N.85 QHS.6: 12 residues within 4Å: Chain B: A.42, E.45, F.46, Y.50, A.53, L.79, N.85, G.87, R.88, V.90, F.140, Y.144 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.42, B:F.46, B:F.46, B:F.46, B:Y.50, B:Y.50, B:Y.50, B:A.53, B:L.79, B:V.90, B:F.140, B:Y.144 Hydrogen bonds: B:N.85

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

EDO.5: 3 residues within 4Å: Chain B: G.4, S.5, M.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.5, B:M.6

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
I

B
J

Bcl-2-like protein 1

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