2Q8Z

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase complexed with 6-amino-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orotidine-monophosphate-decarboxylaseAB342Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF10_0225PF3D7_1023200
EC: 4.1.1.23
Find proteins for Q8IJH3 (Plasmodium falciparum (isolate 3D7))
Explore Q8IJH3 
Go to UniProtKB:  Q8IJH3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NUP
Query on NUP

Download CCD File 
A, B
6-AMINOURIDINE 5'-MONOPHOSPHATE
C9 H14 N3 O9 P
DUFXRFNPGXQQOI-YXZULKJRSA-N
 Ligand Interaction
7PE
Query on 7PE

Download CCD File 
A
2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NUPKi :  2100   nM  PDBBind
NUPKi:  2100   nM  Binding MOAD
NUPKi:  2100   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.497α = 90
b = 83.885β = 90
c = 89.608γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance