Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-iodo-UMP

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Structure-activity relationships of C6-uridine derivatives targeting plasmodia orotidine monophosphate decarboxylase

Bello, A.M.Poduch, E.Liu, Y.Wei, L.Crandall, I.Wang, X.Dyanand, C.Kain, K.C.Pai, E.F.Kotra, L.P.

(2008) J Med Chem 51: 439-448

  • DOI: https://doi.org/10.1021/jm7010673
  • Primary Citation of Related Structures:  
    2Q8Z, 2QAF, 3BAR

  • PubMed Abstract: 

    Malaria, caused by Plasmodia parasites, has re-emerged as a major problem, imposing its fatal effects on human health, especially due to multidrug resistance. In Plasmodia, orotidine 5'-monophosphate decarboxylase (ODCase) is an essential enzyme for the de novo synthesis of uridine 5'-monophosphate. Impairing ODCase in these pathogens is a promising strategy to develop novel classes of therapeutics. Encouraged by our recent discovery that 6-iodo uridine is a potent inhibitor of P. falciparum, we investigated the structure-activity relationships of various C6 derivatives of UMP. 6-Cyano, 6-azido, 6-amino, 6-methyl, 6- N-methylamino, and 6- N, N-dimethylamino derivatives of uridine were evaluated against P. falciparum. The mononucleotides of 6-cyano, 6-azido, 6-amino, and 6-methyl uridine derivatives were studied as inhibitors of plasmodial ODCase. 6-Azidouridine 5'-monophosphate is a potent covalent inhibitor of P. falciparum ODCase. 6-Methyluridine exhibited weak antimalarial activity against P. falciparum 3D7 isolate. 6- N-Methylamino and 6- N, N-dimethylamino uridine derivatives exhibited moderate antimalarial activities.

  • Organizational Affiliation

    Center for Molecular Design and Preformulations and Division of Cell and Molecular Biology, Toronto General Research Institute/University Health Network, MaRS/TMDT, Toronto, ON, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotidine 5' monophosphate decarboxylase
A, B
342Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: ompdc
Find proteins for Q8IJH3 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJH3 
Go to UniProtKB:  Q8IJH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IJH3
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
U5P PDBBind:  2QAF IC50: 4400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.92α = 90
b = 83.849β = 90
c = 89.869γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description