SMTL ID : 7zvf.1 (3 other biounits)

Crystal structure of human cathepsin L in complex with covalently bound CLIK148

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x KXL: (2S)-N-[(2S)-1-(dimethylamino)-1-oxidanylidene-3-phenyl-propan-2-yl]-2-oxidanyl-N'-(2-pyridin-2-ylethyl)butanediamide(Covalent)

KXL.1: 21 residues within 4Å: Chain A: Q.19, G.23, S.24, C.25, W.26, G.67, G.68, L.69, M.70, A.135, A.138, G.139, L.144, M.161, D.162, H.163, G.164, W.189, A.214 Ligands: 1PE.3, PEG.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.69, A:A.135, A:A.138, A:W.189, A:W.189, A:A.214 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162, A:D.162

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

PG4.2: 9 residues within 4Å: Chain A: D.84, E.87, S.88, Y.89, P.90, K.99, Y.100, N.101, Y.104 No protein-ligand interaction detected (PLIP)

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 12 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, A.138, G.139, H.140, E.141, L.144, W.189 Ligands: KXL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.19 Water bridges: A:H.140

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

DMS.4: 3 residues within 4Å: Chain A: P.59, Q.60, D.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.79 Salt bridges: A:D.79 DMS.5: 2 residues within 4Å: Chain A: S.97, C.98 No protein-ligand interaction detected (PLIP)

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

PEG.6: 1 residues within 4Å: Chain A: K.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.103 PEG.7: 6 residues within 4Å: Chain A: K.17, N.18, F.28, E.50, E.86, Y.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18 Water bridges: A:S.47, A:S.47 PEG.8: 9 residues within 4Å: Chain A: G.61, N.62, E.63, N.66, G.67, G.68, L.69, Y.72 Ligands: KXL.1 No protein-ligand interaction detected (PLIP)

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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