CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-car boxylic acid (1-cyano-cyclopropyl)-amide

Experimental Data Snapshot

  • Resolution: 1.00 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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This is version 1.2 of the entry. See complete history


Inhibition of the Cysteine Protease Human Cathepsin L by Triazine Nitriles: AmideHeteroarene pi-Stacking Interactions and Chalcogen Bonding in the S3 Pocket.

Giroud, M.Ivkovic, J.Martignoni, M.Fleuti, M.Trapp, N.Haap, W.Kuglstatter, A.Benz, J.Kuhn, B.Schirmeister, T.Diederich, F.

(2017) ChemMedChem 12: 257-270

  • DOI: https://doi.org/10.1002/cmdc.201600563
  • Primary Citation of Related Structures:  
    5MAE, 5MAJ

  • PubMed Abstract: 

    We report an extensive "heteroarene scan" of triazine nitrile ligands of the cysteine protease human cathepsin L (hCatL) to investigate π-stacking on the peptide amide bond Gly67-Gly68 at the entrance of the S3 pocket. This heteroarene⋅⋅⋅peptide bond stacking was supported by a co-crystal structure of an imidazopyridine ligand with hCatL. Inhibitory constants (K i ) are strongly influenced by the diverse nature of the heterocycles and specific interactions with the local environment of the S3 pocket. Binding affinities vary by three orders of magnitude. All heteroaromatic ligands feature enhanced binding by comparison with hydrocarbon analogues. Predicted energetic contributions from the orientation of the local dipole moments of heteroarene and peptide bond could not be confirmed. Binding of benzothienyl (K i =4 nm) and benzothiazolyl (K i =17 nm) ligands was enhanced by intermolecular C-S⋅⋅⋅O=C interactions (chalcogen bonding) with the backbone C=O of Asn66 in the S3 pocket. The ligands were also tested for the related enzyme rhodesain.

  • Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, 8093, Zurich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathepsin L1220Homo sapiensMutation(s): 0 
Gene Names: CTSLCTSL1
UniProt & NIH Common Fund Data Resources
Find proteins for P07711 (Homo sapiens)
Explore P07711 
Go to UniProtKB:  P07711
PHAROS:  P07711
GTEx:  ENSG00000135047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.00 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.529α = 90
b = 56.64β = 90
c = 73.916γ = 90
Software Package:
Software NamePurpose
XPREPdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Refinement description