SMTL ID : 3inq.1

Crystal structure of BCL-XL in complex with W1191542

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x X0J: 4-[4-(biphenyl-3-ylmethyl)piperazin-1-yl]-N-{[4-({(1R)-3-(dimethylamino)-1-[(phenylsulfanyl)methyl]propyl}amino)-3-nitrophenyl]sulfonyl}benzamide(Non-covalent)

X0J.1: 17 residues within 4Å: Chain A: A.42, E.45, F.46, R.49, Y.50, L.57, E.78, L.79, R.81, N.85, W.86, G.87, R.88, V.90, F.140, Y.144 Ligands: EDO.8 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:Y.50, A:Y.50, A:L.57, A:E.78, A:R.81, A:R.88, A:V.90 Hydrogen bonds: A:N.85, A:N.85, A:W.86, A:G.87, A:Y.144 Water bridges: A:Y.50 Salt bridges: A:E.45 pi-Stacking: A:Y.144 X0J.11: 16 residues within 4Å: Chain B: A.42, E.45, F.46, R.49, Y.50, L.57, V.75, L.79, N.85, W.86, G.87, R.88, V.90, F.95, F.140, Y.144 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.46, B:F.46, B:F.46, B:Y.50, B:Y.50, B:L.57, B:V.75, B:L.79, B:L.79, B:R.88, B:V.90, B:F.95, B:F.95 Hydrogen bonds: B:N.85, B:N.85, B:W.86, B:G.87, B:Y.144 Salt bridges: B:E.45 pi-Stacking: B:Y.144

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

EDO.2: 4 residues within 4Å: Chain A: V.141, E.142, L.143, G.145 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.145 EDO.3: 6 residues within 4Å: Chain A: V.15, S.19, M.32, A.33, K.36 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.19, A:S.19, A:S.30 EDO.4: 8 residues within 4Å: Chain A: S.19, K.36, Q.37, R.40 Chain B: D.16, R.40 Ligands: EDO.3, EDO.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:K.36, A:R.40 Hydrogen bonds: B:D.16, B:R.40, B:R.40 EDO.5: 7 residues within 4Å: Chain A: D.16, R.40 Chain B: S.19, K.36, Q.37, R.40 Ligands: EDO.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.40, A:R.40, B:R.40 EDO.6: 4 residues within 4Å: Chain A: Q.109, V.112, S.113 Chain B: W.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.109 Water bridges: A:V.112 EDO.7: 5 residues within 4Å: Chain A: K.21, Q.24, K.25 Chain B: E.47, F.54 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.21, B:E.47 EDO.8: 3 residues within 4Å: Chain A: N.85, R.88 Ligands: X0J.1 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: R.49, Y.50, R.51, R.52, A.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.51, A:R.52, A:R.52, A:A.53 EDO.10: 1 residues within 4Å: Chain A: R.51 No protein-ligand interaction detected (PLIP) EDO.13: 2 residues within 4Å: Chain B: G.26 Ligands: EDO.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 EDO.14: 3 residues within 4Å: Chain B: G.26, G.145 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 1 residues within 4Å: Chain B: V.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, E.F. et al., Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind ligands. J. Biol. Chem. (2009)

Release Date

2009-09-01

Peptides

Bcl-2-like protein 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bcl-2-like protein 1

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