SMTL ID : 4c52.1

Crystal structure of Bcl-xL in complex with benzoylurea compound (39b)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x X0D: (R)-2-(3-(3-((2,4-DIFLUOROPENYL)ETHYNYL)BENZOYL)-3-PROPYLUREIDO)-3-(ISOBUTYLTHIO) PROPANOIC ACID(Non-covalent)

X0D.1: 17 residues within 4Å: Chain A: F.46, Y.50, A.53, L.57, Q.60, L.61, F.72, V.75, V.76, E.78, L.79, F.92, F.95, G.96, L.99, M.119 Ligands: SO4.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.46, A:L.57, A:Q.60, A:L.61, A:L.61, A:F.72, A:V.76, A:E.78, A:L.79, A:F.95, A:F.95, A:L.99 X0D.12: 19 residues within 4Å: Chain B: F.46, Y.50, R.52, A.53, Q.60, L.61, I.63, F.72, V.75, V.76, E.78, L.79, R.88, A.91, F.92, F.95, G.96, I.115, M.119 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.46, B:Q.60, B:L.61, B:L.61, B:I.63, B:F.72, B:V.76, B:E.78, B:L.79, B:L.79, B:A.91, B:F.92, B:F.95 Salt bridges: B:R.52 pi-Stacking: B:F.95

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

SO4.2: 3 residues within 4Å: Chain A: R.11, V.15, W.29 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.29 Water bridges: A:R.11 Salt bridges: A:R.11 SO4.3: 6 residues within 4Å: Chain A: G.4, S.5, E.12 Chain B: W.29, S.30, M.32 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.30, B:S.30, A:S.5, A:S.5 Water bridges: B:S.19 Salt bridges: B:K.36 SO4.4: 1 residues within 4Å: Chain A: K.106 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.106 SO4.5: 3 residues within 4Å: Chain A: N.85, R.88 Ligands: X0D.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:R.88, A:R.88 Salt bridges: A:R.88 SO4.6: 3 residues within 4Å: Chain A: E.73, N.77, H.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.77 Salt bridges: A:H.126 SO4.13: 2 residues within 4Å: Chain B: N.85, R.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.85 Water bridges: B:R.88 Salt bridges: B:R.88 SO4.14: 4 residues within 4Å: Chain B: A.68, Y.69, R.114, W.118 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.69 Water bridges: B:Q.70 Salt bridges: B:R.114

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

EDO.7: 4 residues within 4Å: Chain A: N.85, W.86, G.87, Y.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.86, A:G.87, A:Y.144 EDO.8: 2 residues within 4Å: Chain A: T.64, P.65 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.67 EDO.9: 5 residues within 4Å: Chain A: G.1, Q.8 Chain B: E.128, Q.132, W.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.1, A:Q.8 EDO.10: 5 residues within 4Å: Chain A: S.19, M.32, A.33, K.36 Chain B: E.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.19 Water bridges: A:D.16, A:D.16 EDO.11: 5 residues within 4Å: Chain A: Q.37, R.40, E.41 Chain B: Y.20, R.40 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.37, A:R.40, B:R.40 Water bridges: A:R.40, B:R.40 EDO.15: 3 residues within 4Å: Chain B: N.85, W.86, G.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.86, B:G.87 Water bridges: B:N.85, B:N.85 EDO.16: 3 residues within 4Å: Chain A: L.3 Chain B: S.30, Q.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.3, B:Q.31 EDO.17: 4 residues within 4Å: Chain B: Q.70, E.73, Q.74, N.77 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.77 EDO.18: 5 residues within 4Å: Chain A: Q.24 Chain B: D.44, E.47, L.48, R.51 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.47, B:E.47, B:R.51, B:R.51 EDO.19: 6 residues within 4Å: Chain A: D.16, R.40 Chain B: S.23, K.36, Q.37, R.40 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.23, A:R.40, A:R.40 EDO.20: 4 residues within 4Å: Chain B: Y.20, S.23, Q.24, Q.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.20, B:S.23, B:N.146 Water bridges: B:Q.24 EDO.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brady, R.M. et al., De-Novo Designed Library of Benzoylureas as Inhibitors of Bcl-Xl: Synthesis, Structural and Biochemical Characterization. J.Med.Chem. (2014)

Release Date

2014-02-05

Peptides

BCL-2-LIKE PROTEIN 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BCL-2-LIKE PROTEIN 1

Related Entries With Identical Sequence