Plasmodium falciparum thymidylate kinase in complex with a (thio)urea- alpha-deoxythymidine inhibitor

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

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Synthesis and Evaluation of Alpha-Thymidine Analogues as Novel Antimalarials.

Cui, H.Carrero-Lerida, J.Silva, A.P.G.Whittingham, J.L.Brannigan, J.A.Ruiz-Perez, L.M.Read, K.D.Wilson, K.S.Gonzalez-Pacanowska, D.Gilbert, I.H.

(2012) J Med Chem 55: 10948

  • DOI: https://doi.org/10.1021/jm301328h
  • Primary Citation of Related Structures:  
    2YOF, 2YOG, 2YOH

  • PubMed Abstract: 

    Plasmodium falciparum thymidylate kinase (PfTMPK) is a key enzyme in pyrimidine nucleotide biosynthesis. 3-Trifluoromethyl-4-chloro-phenyl-urea-α-thymidine has been reported as an inhibitor of Mycobacterium tuberculosis TMPK (MtTMPK). Starting from this point, we designed, synthesized and evaluated a number of thymidine analogues as antimalarials. Both 5'-urea-α- and β-thymidine derivatives were moderate inhibitors of PfTMPK and furthermore showed moderate inhibition of parasite growth. The structure of several enzyme-inhibitor complexes provides a basis for improved inhibitor design. However, we found that certain 5'-urea-α-thymidine analogues had antimalarial activity where inhibition of PfTMPK is not the major mode of action. Optimization of this series resulted in a compound with potent antimalarial activity (EC(50) = 28 nM; CC(50) = 29 μM).

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
210Plasmodium falciparum 3D7Mutation(s): 0 
Find proteins for Q8I4S1 (Plasmodium falciparum (isolate 3D7))
Explore Q8I4S1 
Go to UniProtKB:  Q8I4S1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I4S1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 74X

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxol an-2-yl]methyl]thiourea
C18 H18 Cl F3 N4 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
74X Binding MOAD:  2YOG Ki: 3.10e+4 (nM) from 1 assay(s)
PDBBind:  2YOG Ki: 3.10e+4 (nM) from 1 assay(s)
BindingDB:  2YOG Ki: 3.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.06α = 90
b = 58.79β = 95.78
c = 71.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary