SMTL ID : 7zvf.2 (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: 20 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.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.135, A:A.138, A:L.144, A:W.189, A:W.189, A:A.214 Hydrogen bonds: A:Q.19, A:C.25, A:G.68, A:D.162, A:H.163 Water bridges: A:G.23, A:N.66

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

DMS.2: 5 residues within 4Å: Chain A: R.40, K.124, T.128, V.129, Y.217 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40 DMS.3: 6 residues within 4Å: Chain A: W.7, Y.12, R.40, T.128, V.129, G.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.40, A:R.40

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

1PE.4: 11 residues within 4Å: Chain A: Q.19, G.20, Q.21, C.22, G.23, G.139, H.140, E.141, L.144, W.189 Ligands: KXL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.19

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

NA.5: 4 residues within 4Å: Chain A: Q.75, Q.78, G.111, F.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.75, A:Q.78

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
B

Cathepsin L

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