3IUT

The Crystal Structure of Cruzain in Complex with a Tetrafluorophenoxymethyl Ketone Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors as promising new leads for chagas disease chemotherapy.

Brak, K.Kerr, I.D.Barrett, K.T.Fuchi, N.Debnath, M.Ang, K.Engel, J.C.McKerrow, J.H.Doyle, P.S.Brinen, L.S.Ellman, J.A.

(2010) J.Med.Chem. 53: 1763-1773

  • DOI: 10.1021/jm901633v

  • PubMed Abstract: 
  • A century after discovering that the Trypanosoma cruzi parasite is the etiological agent of Chagas disease, treatment is still plagued by limited efficacy, toxicity, and the emergence of drug resistance. The development of inhibitors of the major T. ...

    A century after discovering that the Trypanosoma cruzi parasite is the etiological agent of Chagas disease, treatment is still plagued by limited efficacy, toxicity, and the emergence of drug resistance. The development of inhibitors of the major T. cruzi cysteine protease, cruzain, has been demonstrated to be a promising drug discovery avenue for this neglected disease. Here we establish that a nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitor substantially ameliorates symptoms of acute Chagas disease in a mouse model with no apparent toxicity. A high-resolution crystal structure confirmed the mode of inhibition and revealed key binding interactions of this novel inhibitor class. Subsequent structure-guided optimization then resulted in inhibitor analogues with improvements in potency despite minimal or no additions in molecular weight. Evaluation of the analogues in cell culture showed enhanced activity. These results suggest that nonpeptidic tetrafluorophenoxymethyl ketone cruzain inhibitors have the potential to fulfill the urgent need for improved Chagas disease chemotherapy.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cruzipain
A
221Trypanosoma cruziMutation(s): 2 
EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi)
Go to UniProtKB:  P25779
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KB2
Query on KB2

Download SDF File 
Download CCD File 
A
(3S)-3-(4-{(1S)-1,2-dimethyl-1-[(quinolin-6-ylmethyl)amino]propyl}-1H-1,2,3-triazol-1-yl)heptan-2-one
C24 H33 N5 O
XHOTUPQHXLRCJV-UPVQGACJSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KB2Ki: 460 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.081α = 90.00
b = 51.451β = 115.50
c = 45.853γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
Blu-Icedata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description