1U9Q

Crystal structure of cruzain bound to an alpha-ketoester


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Development of alpha-keto-based inhibitors of cruzain, a cysteine protease implicated in Chagas disease

Choe, Y.Brinen, L.S.Price, M.S.Engel, J.C.Lange, M.Grisostomi, C.Weston, S.G.Pallai, P.V.Cheng, H.Hardy, L.W.Hartsough, D.S.McMakin, M.Tilton, R.F.Baldino, C.M.Craik, C.S.

(2005) Bioorg.Med.Chem. 13: 2141-2156

  • DOI: 10.1016/j.bmc.2004.12.053

  • PubMed Abstract: 
  • Trypanosoma cruzi, a protozoan parasite, is the causative agent of Chagas disease, a major cause of cardiovascular disease in many Latin American countries. There is an urgent need to develop an improved therapy due to the toxicity of existing drugs ...

    Trypanosoma cruzi, a protozoan parasite, is the causative agent of Chagas disease, a major cause of cardiovascular disease in many Latin American countries. There is an urgent need to develop an improved therapy due to the toxicity of existing drugs and emerging drug resistance. Cruzain, the primary cysteine protease of T. cruzi, is essential for the survival of the parasite in host cells and therefore is an important target for the development of inhibitors as potential therapeutics. A novel series of alpha-ketoamide-, alpha-ketoacid-, alpha-ketoester-, and aldehyde-based inhibitors of cruzain has been developed. The inhibitors were identified by screening protease targeted small molecule libraries and systematically optimizing the P1, P2, P3, and P1' residues using specific structure-guided methods. A total of 20 compounds displayed picomolar potency in in vitro assays and three inhibitors representing different alpha-keto-based inhibitor scaffolds demonstrated anti-trypanosomal activity in cell culture. A 2.3A crystallographic structure of cruzain bound with one of the alpha-ketoester analogs is also reported. The structure and kinetic assay data illustrate the covalent binding, reversible inhibition mechanism of the inhibitor. Information on the compounds reported here will be useful in the development of new lead compounds as potential therapeutic agents for the treatment of Chagas disease and as biological probes to study the role that cruzain plays in the pathology. This study also demonstrates the validity of structure-guided approaches to focused library design and lead compound optimization.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, 600 16th Street, University of California at San Francisco, San Francisco, CA 94143-2280, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cruzipain
X
215Trypanosoma cruziMutation(s): 0 
EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi)
Go to UniProtKB:  P25779
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
186
Query on 186

Download SDF File 
Download CCD File 
X
[1-(1-METHYL-4,5-DIOXO-PENT-2-ENYLCARBAMOYL)-2-PHENYL-ETHYL]-CARBAMIC ACID BENZYL ESTER
C23 H24 N2 O5
NOXVWFAAXREWMI-GURWAVDKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
186Ki: 1103 nM BINDINGMOAD
186IC50: 4.7 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.132 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.720α = 90.00
b = 50.675β = 116.74
c = 45.576γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description