3T64

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • Primary Citation of Related Structures:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
A, B, C
181Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.6.1.23
Find proteins for Q8II92 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8II92
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-(BENZHYDRYLAMINO)-2',5'-DIDEOXYURIDINE
F
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DU3
Query on DU3

Download SDF File 
Download CCD File 
A, B, C
2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine
C22 H23 N3 O4
JJVBLAPDVHVENR-NLWGTHIKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DU3Ki: 200 nM BINDINGMOAD
DU3Ki: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 77.010α = 90.00
b = 77.010β = 90.00
c = 106.280γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Advisory, Structure summary