3T60

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report



Literature

Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.

Hampton, S.E.Baragana, B.Schipani, A.Bosch-Navarrete, C.Musso-Buendia, J.A.Recio, E.Kaiser, M.Whittingham, J.L.Roberts, S.M.Shevtsov, M.Brannigan, J.A.Kahnberg, P.Brun, R.Wilson, K.S.Gonzalez-Pacanowska, D.Johansson, N.G.Gilbert, I.H.

(2011) ChemMedChem 6: 1816-1831

  • DOI: 10.1002/cmdc.201100255
  • Primary Citation of Related Structures:  
    3T60, 3T64, 3T70, 3T6Y

  • PubMed Abstract: 
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is a potential drug target for malaria. We previously reported some 5'-tritylated deoxyuridine analogues (both cyclic and acyclic) as selective inhibitors of the Plasmodium falciparum dUTPase ...

    Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) is a potential drug target for malaria. We previously reported some 5'-tritylated deoxyuridine analogues (both cyclic and acyclic) as selective inhibitors of the Plasmodium falciparum dUTPase. Modelling studies indicated that it might be possible to replace the trityl group with a diphenyl moiety, as two of the phenyl groups are buried, whereas the third is exposed to solvent. Herein we report the synthesis and evaluation of some diphenyl analogues that have lower lipophilicity and molecular weight than the trityl lead compound. Co-crystal structures show that the diphenyl inhibitors bind in a similar manner to the corresponding trityl derivatives, with the two phenyl moieties occupying the predicted buried phenyl binding sites. The diphenyl compounds prepared show similar or slightly lower inhibition of PfdUTPase, and similar or weaker inhibition of parasite growth than the trityl compounds.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Science, University of Dundee, Sir James Black Centre, Dundee DD1 5EH, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase, putativeABC181Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF11_0282PF3D7_1127100
EC: 3.6.1.23
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7))
Explore Q8II92 
Go to UniProtKB:  Q8II92
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUA
Query on DUA

Download CCD File 
A, B, C
2',5'-dideoxy-5'-(tritylamino)uridine
C28 H27 N3 O4
TUZNCXRMWDUVNX-BFLUCZKCSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DUAKi:  1800   nM  Binding MOAD
DUAKi:  200   nM  BindingDB
DUAKi :  200   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.972α = 90
b = 76.972β = 90
c = 106.924γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release