3KKU

Cruzain in complex with a non-covalent ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.

Ferreira, R.S.Simeonov, A.Jadhav, A.Eidam, O.Mott, B.T.Keiser, M.J.McKerrow, J.H.Maloney, D.J.Irwin, J.J.Shoichet, B.K.

(2010) J Med Chem 53: 4891-4905

  • DOI: 10.1021/jm100488w
  • Primary Citation of Related Structures:  
    3KKU

  • PubMed Abstract: 
  • Virtual and high-throughput screens (HTS) should have complementary strengths and weaknesses, but studies that prospectively and comprehensively compare them are rare. We undertook a parallel docking and HTS screen of 197861 compounds against cruzain, a thiol protease target for Chagas disease, looking for reversible, competitive inhibitors ...

    Virtual and high-throughput screens (HTS) should have complementary strengths and weaknesses, but studies that prospectively and comprehensively compare them are rare. We undertook a parallel docking and HTS screen of 197861 compounds against cruzain, a thiol protease target for Chagas disease, looking for reversible, competitive inhibitors. On workup, 99% of the hits were eliminated as false positives, yielding 146 well-behaved, competitive ligands. These fell into five chemotypes: two were prioritized by scoring among the top 0.1% of the docking-ranked library, two were prioritized by behavior in the HTS and by clustering, and one chemotype was prioritized by both approaches. Determination of an inhibitor/cruzain crystal structure and comparison of the high-scoring docking hits to experiment illuminated the origins of docking false-negatives and false-positives. Prioritizing molecules that are both predicted by docking and are HTS-active yields well-behaved molecules, relatively unobscured by the false-positives to which both techniques are individually prone.


    Organizational Affiliation

    Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, California 94158, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CruzipainA215Trypanosoma cruziMutation(s): 0 
EC: 3.4.22.51
UniProt
Find proteins for P25779 (Trypanosoma cruzi)
Explore P25779 
Go to UniProtKB:  P25779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25779
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
B95 Binding MOAD:  3KKU Ki: 2000 (nM) from 1 assay(s)
BindingDB:  3KKU Ki: 2000 (nM) from 1 assay(s)
IC50: 800 (nM) from 1 assay(s)
PDBBind:  3KKU Ki: 2000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.115 
  • R-Value Observed: 0.116 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.978α = 90
b = 82.978β = 90
c = 101.733γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance