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

Human cathepsin L in complex with covalently bound CA-074 methyl ester

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x WRH: methyl (2S)-1-[(2S,3S)-3-methyl-2-[[(3S)-3-oxidanyl-4-oxidanylidene-4-(propylamino)butanoyl]amino]pentanoyl]pyrrolidine-2-carboxylate(Covalent)

WRH.1: 14 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, S.24, C.25, W.26, G.67, G.68, D.162, H.163, G.164, W.189 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.189 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162, A:D.162, A:H.163

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 3 residues within 4Å: Chain A: P.59, Q.60, D.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.60

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

EDO.3: 5 residues within 4Å: Chain A: Y.12, F.39, R.40, G.43 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.12 EDO.5: 4 residues within 4Å: Chain A: K.10, F.39, G.43 Ligands: EDO.3 No protein-ligand interaction detected (PLIP)

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

PEG.4: 6 residues within 4Å: Chain A: S.4, V.5, D.6, W.7, E.9, K.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.6, A:E.9

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

DMS.6: 4 residues within 4Å: Chain A: R.40, T.128, V.129, Y.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40

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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