SMTL ID : 8a4x.2 (3 other biounits)

Crystal structure of human Cathepsin L with covalently bound Calpain inhibitor III

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x L3F: (phenylmethyl) N-[(2S)-3-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]carbamate(Covalent)

L3F.1: 21 residues within 4Å: Chain A: Q.19, C.22, 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, M.161, D.162, H.163, G.164 Ligands: PEG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.63, A:A.135 Hydrogen bonds: A:Q.19, A:G.23, A:C.25, A:G.68, A:G.68, A:D.162

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

PEG.2: 8 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: L3F.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:W.189 PEG.3: 4 residues within 4Å: Chain A: Q.75, Q.78, A.110, G.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.75, A:Q.78 PEG.4: 6 residues within 4Å: Chain A: S.88, Y.89, P.90, K.99, N.101, Y.104 No protein-ligand interaction detected (PLIP) PEG.5: 7 residues within 4Å: Chain A: M.38, T.42, G.82, S.105, V.106, A.107, N.108 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.105, A:A.107, A:N.108

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

2023-07-05

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Cathepsin L

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