SMTL ID : 8ofa.4 (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: PEG.2, VLF.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.189 Hydrogen bonds: A:Q.19, A:C.25

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

PEG.2: 4 residues within 4Å: Chain A: Q.19, G.20, W.189 Ligands: TQ8.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:G.20

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

DMS.3: 4 residues within 4Å: Chain A: P.154, D.155, C.156, S.157 No protein-ligand interaction detected (PLIP) DMS.9: 1 residues within 4Å: Chain A: C.98 No protein-ligand interaction detected (PLIP)

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

EDO.4: 6 residues within 4Å: Chain A: Q.51, D.55, Y.89, E.96, S.97, K.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.55, A:E.96, A:S.97 EDO.6: 4 residues within 4Å: Chain A: Q.118, E.119, R.206, N.207 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.119, A:E.119 Water bridges: A:E.119, A:K.120, A:R.206 EDO.7: 5 residues within 4Å: Chain A: F.39, R.40, K.41, T.42, G.43 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.41 EDO.10: 5 residues within 4Å: Chain A: G.61, E.63, G.67, G.68 Ligands: VLF.11 No protein-ligand interaction detected (PLIP)

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

PGE.5: 4 residues within 4Å: Chain A: N.18, Y.91, E.92, A.93 No protein-ligand interaction detected (PLIP) PGE.8: 6 residues within 4Å: Chain A: D.84, S.88, Y.89, P.90, K.99, Y.104 No protein-ligand interaction detected (PLIP)

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

VLF.11: 14 residues within 4Å: Chain A: 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, EDO.10 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
D

Cathepsin L

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