SMTL ID : 8b4f.1 (4 other biounits)

Crystal structure of human cathepsin L forming a thiohemiacetal with N-Boc-2-aminoacetaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x OYU: ~{tert}-butyl ~{N}-(2-hydroxyethyl)carbamate(Covalent)

OYU.1: 13 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.67, G.68, L.69, A.135, M.161, D.162, H.163, G.164 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.69 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 8 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, Y.100, N.101, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.88

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

DMS.3: 2 residues within 4Å: Chain A: S.97, C.98 No protein-ligand interaction detected (PLIP)

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

EDO.4: 7 residues within 4Å: Chain A: D.178, N.179, N.180, K.181, K.203, D.204, R.205 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:K.181 Water bridges: A:N.180, A:K.203 EDO.6: 7 residues within 4Å: Chain A: C.56, S.57, P.59, Q.60, Y.76, D.79, N.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60, A:Q.60, A:N.80

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

PEG.5: 8 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, L.144, W.189 Ligands: NA.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.22

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

NA.7: 3 residues within 4Å: Chain A: Q.60, Q.75, D.79 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.79 NA.8: 2 residues within 4Å: Chain A: Q.21 Ligands: PEG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.21, A:Q.21

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

2023-09-27

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin L

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