2YOG | pdb_00002yog

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 74XClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDYLATE KINASE
A, B
210Plasmodium falciparum 3D7Mutation(s): 0 
EC: 2.7.4.9 (PDB Primary Data), 2.7.4.8 (UniProt)
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
74X
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
IJDGQXGQAWBJEG-MJBXVCDLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
74X BindingDB:  2YOG Ki: 3.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
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
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 74XClick on this verticalbar to view details

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