1VYQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.str.2004.11.015

  • 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 identif ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
A, B, C
173Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.6.1.23
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8II92
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUX
Query on DUX

Download SDF File 
Download CCD File 
A, B, C
2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE
1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE
C28 H25 F N2 O4
GJNIPWYJQUGERM-BFLUCZKCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DUXKi: 5000 nM (100) BINDINGDB
DUXKi: 4980 nM BINDINGMOAD
DUXKi: 4980 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.191 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 62.830α = 90.00
b = 62.830β = 90.00
c = 121.527γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
DENZOdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2005-05-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance