SMTL ID : 7zxa.3 (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

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

E6D.1: 23 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: PEG.3, PGE.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.26, A:E.63, 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

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

PEG.2: 5 residues within 4Å: Chain A: F.39, R.40, K.41, T.42, G.43 No protein-ligand interaction detected (PLIP) PEG.3: 10 residues within 4Å: Chain A: A.138, G.139, H.140, E.141, L.144, D.162, H.163, W.189 Ligands: E6D.1, PGE.5 No protein-ligand interaction detected (PLIP) PEG.4: 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 PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 9 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: E6D.1, PEG.3 No protein-ligand interaction detected (PLIP)

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

EDO.6: 10 residues within 4Å: Chain A: L.69, M.70, D.71, F.74, D.114, S.133, V.134, A.214, A.215, S.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.70, A:D.71, A:S.133 EDO.7: 6 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18, A:N.18

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
C

Cathepsin L

Related Entries With Identical Sequence