SMTL ID : 7zxa.2 (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: 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: PEG.4 9 PLIP interactions: 9 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 Salt bridges: A:H.163

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

DMS.2: 3 residues within 4Å: Chain A: P.59, Q.60, D.79 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.79 DMS.3: 7 residues within 4Å: Chain A: W.7, Y.12, R.40, T.128, V.129, G.130 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40

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

PEG.4: 8 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: E6D.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.21 Water bridges: A:Q.21, A:G.23 PEG.5: 9 residues within 4Å: Chain A: P.2, S.4, V.5, D.6, W.7, E.9, K.10, A.127 Ligands: DMS.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.6, A:A.127 PEG.6: 6 residues within 4Å: Chain A: M.38, K.41, T.42, A.107, N.108, V.220 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.108

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

EDO.7: 7 residues within 4Å: Chain A: D.84, S.88, Y.89, K.99, Y.100, N.101, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Falke, S. et al., Structural elucidation of antiviral cathepsin L inhibitors. To Be Published

Release Date

2023-05-31

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cathepsin L

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