Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Optimization of Triazine Nitriles as Rhodesain Inhibitors: Structure-Activity Relationships, Bioisosteric Imidazopyridine Nitriles, and X-Ray Crystal Structure Analysis with Human Cathepsin L

Ehmke, V.Winkler, E.Banner, D.W.Haap, W.Schweizer, W.B.Rottmann, M.Kaiser, M.Freymond, C.Schirmeister, T.Diederich, F.

(2013) ChemMedChem 8: 967

  • DOI: https://doi.org/10.1002/cmdc.201300112
  • Primary Citation of Related Structures:  
    4AXL, 4AXM

  • PubMed Abstract: 

    The cysteine protease rhodesain of Trypanosoma brucei parasites causing African sleeping sickness has emerged as a target for the development of new drug candidates. Based on a triazine nitrile moiety as electrophilic headgroup, optimization studies on the substituents for the S1, S2, and S3 pockets of the enzyme were performed using structure-based design and resulted in inhibitors with inhibition constants in the single-digit nanomolar range. Comprehensive structure-activity relationships clarified the binding preferences of the individual pockets of the active site. The S1 pocket tolerates various substituents with a preference for flexible and basic side chains. Variation of the S2 substituent led to high-affinity ligands with inhibition constants down to 2 nM for compounds bearing cyclohexyl substituents. Systematic investigations on the S3 pocket revealed its potential to achieve high activities with aromatic vectors that undergo stacking interactions with the planar peptide backbone forming part of the pocket. X-ray crystal structure analysis with the structurally related enzyme human cathepsin L confirmed the binding mode of the triazine ligand series as proposed by molecular modeling. Sub-micromolar inhibition of the proliferation of cultured parasites was achieved for ligands decorated with the best substituents identified through the optimization cycles. In cell-based assays, the introduction of a basic side chain on the inhibitors resulted in a 35-fold increase in antitrypanosomal activity. Finally, bioisosteric imidazopyridine nitriles were studied in order to prevent off-target effects with unselective nucleophiles by decreasing the inherent electrophilicity of the triazine nitrile headgroup. Using this ligand, the stabilization by intramolecular hydrogen bonding of the thioimidate intermediate, formed upon attack of the catalytic cysteine residue, compensates for the lower reactivity of the headgroup. The imidazopyridine nitrile ligand showed excellent stability toward the thiol nucleophile glutathione in a quantitative in vitro assay and fourfold lower cytotoxicity than the parent triazine nitrile.

  • Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zürich, Zürich, 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07711
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on V65

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth F]
N [auth I]
P [auth L]
H [auth A],
J [auth B],
L [auth F],
N [auth I],
P [auth L],
R [auth O]
C21 H27 Cl N6 O2
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth F]
M [auth I]
O [auth L]
G [auth A],
I [auth B],
K [auth F],
M [auth I],
O [auth L],
Q [auth O]
C3 H8 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
V65 PDBBind:  4AXM Ki: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.842α = 90
b = 134.781β = 90
c = 140.92γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata 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: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2013-06-12
    Changes: Database references