SMTL ID : 3zlr.1

Crystal structure of BCL-XL in complex with inhibitor (WEHI-539)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x X0B: 5-[3-[4-(aminomethyl)phenoxy]propyl]-2-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]-1,3-thiazole-4-carboxylic acid(Non-covalent)

X0B.1: 22 residues within 4Å: Chain A: A.42, E.45, F.46, Y.50, R.51, F.54, S.55, D.56, L.57, T.58, E.78, L.79, R.81, N.85, G.87, R.88, A.91, S.94, F.95, A.98, Y.144 Ligands: EDO.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:E.45, A:F.46, A:F.46, A:Y.50, A:F.54, A:F.54, A:L.57, A:T.58, A:L.79, A:F.95, A:A.98 Hydrogen bonds: A:S.55, A:L.57, A:N.85 Water bridges: A:E.45, A:Y.50, A:R.88, A:R.88, A:R.88, A:R.88, A:Y.144 Salt bridges: A:R.88 pi-Stacking: A:F.95, A:Y.144 X0B.5: 20 residues within 4Å: Chain B: A.42, E.45, F.46, Y.50, R.51, F.54, S.55, D.56, L.57, E.78, L.79, R.81, N.85, G.87, R.88, A.91, S.94, F.95, A.98, Y.144 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.46, B:F.46, B:F.46, B:Y.50, B:Y.50, B:F.54, B:F.54, B:L.57, B:L.79, B:F.95, B:A.98, B:Y.144 Hydrogen bonds: B:S.55, B:L.57, B:N.85 Water bridges: B:R.88, B:R.88 Salt bridges: B:R.88 pi-Stacking: B:F.95

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

EDO.2: 5 residues within 4Å: Chain A: N.77, F.80, V.84, Y.122, H.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.77 EDO.3: 2 residues within 4Å: Chain A: E.45 Ligands: X0B.1 No protein-ligand interaction detected (PLIP)

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

SO4.4: 4 residues within 4Å: Chain A: N.85, W.86, G.87, Y.144 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.86, A:G.87, A:Y.144 Water bridges: A:Y.144 SO4.6: 4 residues within 4Å: Chain B: N.85, W.86, G.87, Y.144 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.86, B:G.87, B:Y.144 SO4.7: 4 residues within 4Å: Chain A: N.124 Chain B: S.9, N.10, R.11 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.9, B:N.10, B:R.11, A:N.124, A:N.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lessene, G.L. et al., Structure-Guided Design of a Selective Bcl-Xl Inhibitor. Nat.Chem.Biol. (2013)

Release Date

2013-04-24

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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