SMTL ID : 3sp7.1

Crystal Structure of Bcl-xL bound to BM903

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x 03B: 5-(4-chlorophenyl)-4-{3-[4-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]amino}phenyl)piperazin-1-yl]phenyl}-1,2-dimethyl-1H-pyrrole-3-carboxylic acid(Non-covalent)

03B.1: 23 residues within 4Å: Chain A: E.59, F.60, R.63, Y.64, A.67, F.68, V.89, E.92, L.93, R.95, N.99, W.100, G.101, R.102, V.104, A.105, S.108, F.109, A.112, F.154, Y.158, N.161, A.162 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.60, A:F.60, A:F.60, A:Y.64, A:Y.64, A:A.67, A:E.92, A:L.93, A:L.93, A:V.104, A:F.109, A:Y.158 Hydrogen bonds: A:W.100, A:G.101 Water bridges: A:R.95, A:R.95 Salt bridges: A:E.59, A:R.95 pi-Stacking: A:F.109

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: E.10, D.14 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.10, A:D.14, A:D.14, H2O.3, H2O.6 ZN.3: 3 residues within 4Å: Chain A: K.23, E.61 Ligands: ACT.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.5 ZN.4: 3 residues within 4Å: Chain A: E.87, H.140 Ligands: ACT.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.87, A:E.87, A:H.140, ACT.8 ZN.5: 1 residues within 4Å: Chain A: E.147 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.147

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain A: K.23, E.61, F.68, A.112, V.115 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.68, A:A.112, A:V.115 Salt bridges: A:K.23 ACT.7: 5 residues within 4Å: Chain A: R.9, V.13, W.27, S.31, D.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.31 Salt bridges: A:R.9 ACT.8: 3 residues within 4Å: Chain A: E.87, H.140 Ligands: ZN.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.84 Salt bridges: A:H.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, H. et al., Structure-based design of a new class of potent Bcl-2/Bcl-xL inhibitors. To be Published

Release Date

2012-07-04

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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