5MAJ

CATHEPSIN L IN COMPLEX WITH 4-[cyclopentyl(imidazo[1,2-a]pyridin-2-ylmethyl)amino]-6-morpholino-1,3,5-triazine-2-carbonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1002/cmdc.201600563
  • Primary Citation of Related Structures:  

  • 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 ...

    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 (Ki ) 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 (Ki =4 nm) and benzothiazolyl (Ki =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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cathepsin L1
A
220Homo sapiensMutation(s): 0 
Gene Names: CTSL (CTSL1)
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Go to Gene View: CTSL
Go to UniProtKB:  P07711
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
7KH
Query on 7KH

Download SDF File 
Download CCD File 
A
~{N}-cyclopentyl-~{N}-(imidazo[1,2-a]pyridin-2-ylmethyl)-4-(iminomethyl)-6-morpholin-4-yl-1,3,5-triazin-2-amine
C21 H26 N8 O
DGSRSTVIVXXYMJ-LPYMAVHISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.136 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.700α = 90.00
b = 57.061β = 90.00
c = 75.266γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XPREPdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references