SMTL ID : 8ofa.1 (3 other biounits)

Crystal structure of human cathepsin L interacting with tosyl phenylalanyl chloromethyl ketone (TPCK)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x TQ8: N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide(Covalent)

TQ8.1: 10 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, G.139, D.162, H.163, W.189 Ligands: DMS.8, VLF.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.189 Hydrogen bonds: A:Q.19, A:C.25

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

EDO.2: 4 residues within 4Å: Chain A: A.1, P.2, A.127, T.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.127

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

PEG.3: 6 residues within 4Å: Chain A: G.61, E.63, N.66, G.68, L.69 Ligands: VLF.10 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: Q.118, E.119, R.206, N.207 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.119 Water bridges: A:E.119, A:N.207

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

DMS.4: 3 residues within 4Å: Chain A: S.177, D.178, N.179 No protein-ligand interaction detected (PLIP) DMS.7: 3 residues within 4Å: Chain A: P.59, Q.60, D.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.60, A:D.79 Salt bridges: A:D.79 DMS.8: 3 residues within 4Å: Chain A: Q.21, W.189 Ligands: TQ8.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.189

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

PGE.5: 4 residues within 4Å: Chain A: S.88, Y.89, K.99, Y.104 No protein-ligand interaction detected (PLIP)

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.6: 2 residues within 4Å: Chain A: K.103, Y.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.103

1 x VLF: 4-methyl-~{N}-[(2~{S})-4-oxidanyl-3-oxidanylidene-1-phenyl-butan-2-yl]benzenesulfonamide(Non-covalent)

VLF.10: 15 residues within 4Å: Chain A: G.23, C.25, N.66, G.67, G.68, L.69, M.70, A.135, M.161, D.162, H.163, G.164, A.214 Ligands: TQ8.1, PEG.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.69, A:A.135, A:A.214 Hydrogen bonds: A:G.68

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

2023-11-29

Peptides

Cathepsin L: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cathepsin L

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