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 

wwPDB Validation 3D Report Full Report


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

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cruzipain
A
215Trypanosoma cruziMutation(s): 0 
EC: 3.4.22.51
Find proteins for P25779 (Trypanosoma cruzi)
Go to UniProtKB:  P25779
Small Molecules
Ligands 3 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
Z22
Query on Z22

Download SDF File 
Download CCD File 
A
S-methyl methanesulfonothioate
S-Methyl methanethiosulfonate
C2 H6 O2 S2
XYONNSVDNIRXKZ-UHFFFAOYSA-N
 Ligand Interaction
B95
Query on B95

Download SDF File 
Download CCD File 
A
N-[2-(1H-benzimidazol-2-yl)ethyl]-2-(2-bromophenoxy)acetamide
C17 H16 Br N3 O2
XWFRNTHGPRGCNS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B95Ki: 2000 nM (100) BINDINGDB
B95IC50: 800 nM (100) BINDINGDB
B95Ki: 2000 nM BINDINGMOAD
B95Ki: 2000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.115 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 82.978α = 90.00
b = 82.978β = 90.00
c = 101.733γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
MOSFLMdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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