SMTL ID : 3zln.1

Crystal structure of BCL-XL in complex with inhibitor (Compound 3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

monomer

Ligands

1 x H0Y: 6-[(8E)-8-(1,3-benzothiazol-2-ylhydrazinylidene)-6,7-dihydro-5H-naphthalen-2-yl]pyridine-2-carboxylic acid(Non-covalent)

H0Y.1: 18 residues within 4Å: Chain A: F.61, R.66, F.69, S.70, D.71, L.72, T.73, E.93, L.94, R.96, N.100, G.102, R.103, A.106, S.109, F.110, A.113 Ligands: SO4.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.61, A:F.61, A:F.69, A:F.69, A:F.69, A:T.73, A:L.94, A:R.103, A:A.106, A:F.110, A:A.113 Hydrogen bonds: A:S.70, A:L.72, A:N.100 Water bridges: A:R.103, A:R.103 Salt bridges: A:R.103 pi-Stacking: A:F.110

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

SO4.2: 4 residues within 4Å: Chain A: F.69, S.70, R.96 Ligands: H0Y.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.70 Salt bridges: A:R.96

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

EDO.3: 4 residues within 4Å: Chain A: Q.23, K.24, D.59, E.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.24, A:E.62 Water bridges: A:K.24, A:E.62, A:E.62 EDO.4: 5 residues within 4Å: Chain A: N.100, W.101, G.102, W.145, Y.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.101, A:G.102, A:Y.159 Water bridges: A:Y.159 EDO.5: 6 residues within 4Å: Chain A: Y.19, Q.52, R.55, E.56 Ligands: EDO.6, EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.55, A:E.56 EDO.6: 4 residues within 4Å: Chain A: Y.19, Q.23 Ligands: EDO.5, EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.23 EDO.7: 4 residues within 4Å: Chain A: Y.19, R.55 Ligands: EDO.5, EDO.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.55

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BCL-2-LIKE PROTEIN 1

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