2YOF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1021/jm301328h
  • Primary Citation of Related Structures:  

  • 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 t ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE KINASE
A, B, C
210Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 2.7.4.9
Find proteins for Q8I4S1 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I4S1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
74W
Query on 74W

Download SDF File 
Download CCD File 
A, B, C
1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]thiourea
(THIO)UREA-BETA-DEOXYTHYMIDINE DERIVATIVE
C18 H18 Cl F3 N4 O4 S
IJDGQXGQAWBJEG-BFHYXJOUSA-N
 Ligand Interaction
TAM
Query on TAM

Download SDF File 
Download CCD File 
A, B
TRIS(HYDROXYETHYL)AMINOMETHANE
C7 H17 N O3
GKODZWOPPOTFGA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
74WKi: 25000 nM (100) BINDINGDB
74WKi: 25000 nM BINDINGMOAD
74WKi: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.639α = 90.00
b = 109.639β = 90.00
c = 121.892γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release