SMTL ID : 4c5d.1

Crystal structure of Bcl-xL in complex with benzoylurea compound (42)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x X0R: (R)-3-(4-BROMOBENZYLTHIO)-2-(3-(3-((2,4-DIFLUOROPHENYL)ETHYNYL)BENZOYL)-3-PROPYLUREIDO)PROPANOIC ACID(Non-covalent)

X0R.1: 20 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, G.87, R.88, A.91, F.92, F.95, G.96, L.99, M.119 Ligands: SO4.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: 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:A.91, A:F.92, A:F.95, A:F.95, A:L.99 Water bridges: A:R.88, A:R.88 pi-Stacking: A:F.46, A:Y.50 X0R.10: 18 residues within 4Å: Chain B: F.46, Y.50, R.52, A.53, Q.60, L.61, I.63, F.72, V.75, E.78, L.79, G.87, R.88, F.92, F.95, G.96, M.119 Ligands: SO4.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.46, B:F.46, B:Q.60, B:L.61, B:L.61, B:I.63, B:F.72, B:E.78, B:L.79, B:F.92, B:F.95 Hydrogen bonds: B:R.52 pi-Stacking: B:Y.50, B:F.95 X0R.19: 20 residues within 4Å: Chain C: F.46, Y.50, A.53, L.57, Q.60, L.61, F.72, V.75, V.76, E.78, L.79, G.87, R.88, A.91, F.92, F.95, G.96, L.99, M.119 Ligands: SO4.21 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:L.57, C:Q.60, C:L.61, C:L.61, C:F.72, C:V.76, C:E.78, C:L.79, C:A.91, C:F.92, C:F.95, C:F.95, C:L.99 Water bridges: C:R.88, C:R.88 pi-Stacking: C:F.46, C:Y.50 X0R.28: 18 residues within 4Å: Chain D: F.46, Y.50, R.52, A.53, Q.60, L.61, I.63, F.72, V.75, E.78, L.79, G.87, R.88, F.92, F.95, G.96, M.119 Ligands: SO4.29 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.46, D:F.46, D:Q.60, D:L.61, D:L.61, D:I.63, D:F.72, D:E.78, D:L.79, D:F.92, D:F.95 Hydrogen bonds: D:R.52 pi-Stacking: D:Y.50, D:F.95

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

SO4.2: 8 residues within 4Å: Chain A: G.4, S.5, E.12 Chain B: V.15, W.29, S.30, M.32 Ligands: EDO.14 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.5, A:E.12, B:W.29, B:S.30 Water bridges: A:M.6 Salt bridges: B:K.36 SO4.3: 3 residues within 4Å: Chain A: N.85, R.88 Ligands: X0R.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.85 Water bridges: A:N.85, A:R.88 Salt bridges: A:R.88 SO4.4: 9 residues within 4Å: Chain A: W.29, S.30, M.32, A.33 Chain D: G.4, S.5, M.6, S.7 Ligands: SO4.31 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:M.6, D:S.7, A:S.30, A:S.30, A:A.33 Water bridges: A:Q.31 Salt bridges: A:K.36 SO4.11: 3 residues within 4Å: Chain B: N.85, R.88 Ligands: X0R.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.85 Water bridges: B:N.85, B:R.88 Salt bridges: B:R.88 SO4.12: 3 residues within 4Å: Chain B: N.85, W.86, G.87 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.85, B:W.86, B:G.87 Water bridges: B:N.85, B:Y.144, B:Y.144 SO4.13: 6 residues within 4Å: Chain B: M.6, S.7 Chain C: R.11, V.15, W.29 Ligands: SO4.22 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.29 Salt bridges: C:R.11 SO4.20: 8 residues within 4Å: Chain C: G.4, S.5, E.12 Chain D: V.15, W.29, S.30, M.32 Ligands: EDO.32 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.5, C:E.12, D:W.29, D:S.30 Water bridges: C:M.6 Salt bridges: D:K.36 SO4.21: 3 residues within 4Å: Chain C: N.85, R.88 Ligands: X0R.19 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.85 Water bridges: C:N.85, C:R.88 Salt bridges: C:R.88 SO4.22: 9 residues within 4Å: Chain B: G.4, S.5, M.6, S.7 Chain C: W.29, S.30, M.32, A.33 Ligands: SO4.13 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:M.6, B:S.7, C:S.30, C:S.30, C:A.33 Water bridges: C:Q.31 Salt bridges: C:K.36 SO4.29: 3 residues within 4Å: Chain D: N.85, R.88 Ligands: X0R.28 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.85 Water bridges: D:N.85, D:R.88 Salt bridges: D:R.88 SO4.30: 3 residues within 4Å: Chain D: N.85, W.86, G.87 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.85, D:W.86, D:G.87 Water bridges: D:N.85 SO4.31: 6 residues within 4Å: Chain A: R.11, V.15, W.29 Chain D: M.6, S.7 Ligands: SO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.29 Salt bridges: A:R.11

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

EDO.5: 2 residues within 4Å: Chain A: T.64, P.65 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.16, R.40 Chain B: S.23, K.36, Q.37, R.40 Ligands: EDO.14 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: N.85, W.86, G.87, Y.144 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: S.19, Y.20, A.33, Q.37, R.40 Chain B: D.16, R.40 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: N.77, V.84, Y.122, H.126 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: S.19, A.33, K.36 Ligands: SO4.2, EDO.6 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain B: Y.20, Q.24 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: R.49, Y.50, R.52 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: Y.69, R.114, W.118 Ligand excluded by PLIP EDO.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP EDO.23: 2 residues within 4Å: Chain C: T.64, P.65 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: D.16, R.40 Chain D: S.23, K.36, Q.37, R.40 Ligands: EDO.32 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: N.85, W.86, G.87, Y.144 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: S.19, Y.20, A.33, Q.37, R.40 Chain D: D.16, R.40 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: N.77, V.84, Y.122, H.126 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain D: S.19, A.33, K.36 Ligands: SO4.20, EDO.24 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain D: Y.20, Q.24 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain D: R.49, Y.50, R.52 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain D: Y.69, R.114, W.118 Ligand excluded by PLIP EDO.36: 0 residues within 4Å: (No contacts) Ligand excluded by 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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

BCL-2-LIKE PROTEIN 1

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