1VYQ

Novel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial drug design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Dutpase as a Platform for Antimalarial Drug Design: Structural Basis for the Selectivity of a Class of Nucleoside Inhibitors.

Whittingham, J.L.Leal, I.Nguyen, C.Kasinathan, G.Bell, E.Jones, A.F.Berry, C.Benito, A.Turkenburg, J.P.Dodson, E.J.Ruiz Perez, L.M.Wilkinson, A.J.Johansson, N.G.Brun, R.Gilbert, I.H.Gonzalez Pacanowska, D.Wilson, K.S.

(2005) Structure 13: 329

  • DOI: https://doi.org/10.1016/j.str.2004.11.015
  • Primary Citation of Related Structures:  
    1VYQ

  • PubMed Abstract: 

    Pyrimidine metabolism is a major route for therapeutic intervention against malaria. Here we report inhibition and structural studies on the deoxyuridine nucleotidohydrolase from the malaria parasite Plasmodium falciparum (PfdUTPase). We have identified a series of triphenylmethane derivatives of deoxyuridine with antimalarial activity in vitro which inhibit specifically the Plasmodium dUTPase versus the human enzyme. A 2.4 Angstrom crystal structure of PfdUTPase in complex with one of these inhibitors reveals an atypical trimeric enzyme in which the triphenylmethane derivative can be seen to select for PfdUTPase by way of interactions between the trityl group and the side chains of residues Phe46 and Ile117. Immunofluorescence microscopy studies of parasitized red blood cells reveal that enzyme concentrations are highest during the trophozoite/schizont stages, suggesting that PfdUTPase has a major role in DNA replication. Taken together the data show that PfdUTPase may be considered as an antimalarial drug target.


  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
A, B, C
173Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.6.1.23
UniProt
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7))
Explore Q8II92 
Go to UniProtKB:  Q8II92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8II92
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DUX PDBBind:  1VYQ Ki: 4980 (nM) from 1 assay(s)
Binding MOAD:  1VYQ Ki: 4980 (nM) from 1 assay(s)
BindingDB:  1VYQ Ki: 5000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.196 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.83α = 90
b = 62.83β = 90
c = 121.527γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description