SMTL ID : 3wiz.1

Crystal structure of Bcl-xL in complex with compound 10

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x LC6: 7-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]carbamoyl}-2-methylphenyl)-3-[3-(naphthalen-1-yloxy)propyl]pyrazolo[1,5-a]pyridine-2-carboxylic acid(Non-covalent)

LC6.1: 17 residues within 4Å: Chain A: A.53, E.56, F.57, R.60, Y.61, L.68, V.86, E.89, L.90, N.96, W.97, G.98, R.99, V.101, A.102 Chain B: F.151, Y.155 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.57, A:F.57, A:Y.61, A:Y.61, A:Y.61, A:V.86, A:E.89, A:L.90, A:V.101, A:A.102 Hydrogen bonds: A:N.96, A:W.97, A:G.98 Salt bridges: A:E.56, A:R.99 LC6.3: 18 residues within 4Å: Chain A: F.151, Y.155 Chain B: A.53, E.56, F.57, R.60, Y.61, F.65, L.68, V.86, L.90, N.96, W.97, G.98, R.99, V.101, A.102, F.106 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.57, B:F.57, B:Y.61, B:Y.61, B:F.65, B:L.68, B:L.90, B:R.99, B:V.101, B:A.102 Hydrogen bonds: B:W.97, B:G.98 Salt bridges: B:E.56, B:R.99 pi-Stacking: B:F.106, A:Y.155

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: Y.80, Q.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.80, A:Q.81, A:Q.81 PO4.4: 3 residues within 4Å: Chain B: A.79, Y.80, Q.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.80, B:Q.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, Y. et al., Discovery of potent Mcl-1/Bcl-xL dual inhibitors by using a hybridization strategy based on structural analysis of target proteins. J.Med.Chem. (2013)

Release Date

2013-11-27

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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