SMTL ID : 2r9c.1

Calpain 1 proteolytic core inactivated by ZLAK-3001, an alpha-ketoamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: V.74, G.76, D.81, E.160 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.74, A:G.76, A:D.81, A:E.160, H2O.1 CA.2: 6 residues within 4Å: Chain A: E.277, D.284, V.302, M.304, D.306, E.308 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.277, A:D.284, A:M.304, A:E.308, H2O.2

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

CL.3: 1 residues within 4Å: Chain A: Q.15 Ligand excluded by PLIP CL.4: 1 residues within 4Å: Chain A: S.40 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: Q.71, F.72, S.115, F.116, Q.117 Ligand excluded by PLIP

1 x GRD: benzyl (S)-1-((2S,3S)-1-(3-(6-amino-9H-purin-9-yl)propylamino)-2-hydroxy-1-oxopentan-3-ylamino)-4-methyl-1-oxopentan-2-ylcarbamate(Non-covalent)

GRD.6: 16 residues within 4Å: Chain A: Q.84, G.85, L.87, G.88, D.89, C.90, W.91, G.182, G.183, T.185, S.226, G.246, H.247, A.248, W.273, E.275 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:A.248 Hydrogen bonds: A:Q.84, A:C.90, A:G.182, A:G.183, A:G.183, A:G.246, A:H.247, A:E.275, A:E.275 Water bridges: A:G.246, A:H.247 pi-Stacking: A:W.273, A:W.273, A:W.273

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: L.66, L.67, G.148, K.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.66, A:G.148 GOL.8: 4 residues within 4Å: Chain A: Q.32, R.62, E.65, L.142 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.62, A:E.65 Water bridges: A:L.30, A:L.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, J. et al., Cocrystal structures of primed side-extending alpha-ketoamide inhibitors reveal novel calpain-inhibitor aromatic interactions. J.Med.Chem. (2008)

Release Date

2008-08-26

Peptides

Calpain-1 catalytic subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Calpain-1 catalytic subunit

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