SMTL ID : 7qkb.3 (3 other biounits)

Crystal structure of human Cathepsin L in complex with covalently bound GC376

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: F.39, R.40, T.42, G.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.42 PEG.2: 7 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, N.101, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: D.137, H.140, C.156, S.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.137, A:H.140, A:S.157

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

PG4.4: 11 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, G.139, L.144, D.162, H.163, W.189 Ligands: UED.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21, A:D.162

1 x UED: N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide(Covalent)

UED.5: 23 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.61, N.62, E.63, C.65, 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: PG4.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.63, A:L.69 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:G.68, A:D.162, A:H.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reinke, P.Y.A. et al., Calpeptin is a potent cathepsin inhibitor and drug candidate for SARS-CoV-2 infections. Commun Biol (2023)

Release Date

2022-12-28

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Cathepsin L

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