SMTL ID : 7zxa.4 (3 other biounits)

Crystal structure of human cathepsin L with covalently bound aloxistatin (E-64D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 4 residues within 4Å: Chain A: P.154, D.155, C.156, S.157 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.157 DMS.3: 4 residues within 4Å: Chain A: S.4, G.171, F.172, Y.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.172, A:Y.182 pi-Cation interactions: A:F.172

1 x E6D: ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate(Covalent)

E6D.2: 22 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.61, N.62, E.63, N.66, G.67, G.68, L.69, M.70, Y.72, A.135, I.136, M.161, D.162, H.163, G.164, W.189 Ligands: P6G.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.72, A:A.135, A:W.189 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:G.68, A:D.162, A:D.162 Salt bridges: A:H.163

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 14 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, A.138, G.139, H.140, E.141, L.144, D.162, H.163, W.189 Ligands: E6D.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.140

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 8 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, Y.100, N.101, Y.104 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: D.178, N.179, K.181, K.203, D.204, R.205 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.181 Water bridges: A:K.120, A:D.204

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 7 residues within 4Å: Chain A: N.18, Q.19, G.20, Y.91, E.92, A.93 Ligands: EDO.8 No protein-ligand interaction detected (PLIP)

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

EDO.8: 7 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 Ligands: PGE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:N.18, A:E.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falke, S. et al., Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors. J.Med.Chem. (2024)

Release Date

2023-05-31

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Cathepsin L

Related Entries With Identical Sequence