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 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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, 3T6Y, 3T70

  • 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. 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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Deoxyuridine 5'-triphosphate nucleotidohydrolase, putativeA, B, C181Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF11_0282PF3D7_1127100
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DUA Binding MOAD:  3T60 Ki: 200 (nM) from 1 assay(s)
BindingDB:  3T60 Ki: 200 (nM) from 1 assay(s)
PDBBind:  3T60 Ki: 200 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

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