3S9Y | pdb_00003s9y

Crystal Structure of P. falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP in space group P21, produced from 5-fluoro-6-azido-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents.

Bello, A.M.Konforte, D.Poduch, E.Furlonger, C.Wei, L.Liu, Y.Lewis, M.Pai, E.F.Paige, C.J.Kotra, L.P.

(2009) J Med Chem 52: 1648-1658

  • DOI: https://doi.org/10.1021/jm801224t
  • Primary Citation of Related Structures:  
    3G3D, 3G3M, 3S9Y

  • PubMed Abstract: 

    A series of 6-substituted and 5-fluoro-6-substituted uridine derivatives were synthesized and evaluated for their potential as anticancer agents. The designed molecules were synthesized from either fully protected uridine or the corresponding 5-fluorouridine derivatives. The mononucleotide derivatives were used for enzyme inhibition investigations against ODCase. Anticancer activities of all the synthesized derivatives were evaluated using the nucleoside forms of the inhibitors. 5-Fluoro-UMP was a very weak inhibitor of ODCase. 6-Azido-5-fluoro and 5-fluoro-6-iodo derivatives are covalent inhibitors of ODCase, and the active site Lys145 residue covalently binds to the ligand after the elimination of the 6-substitution. Among the synthesized nucleoside derivatives, 6-azido-5-fluoro, 6-amino-5-fluoro, and 6-carbaldehyde-5-fluoro derivatives showed potent anticancer activities in cell-based assays against various leukemia cell lines. On the basis of the overall profile, 6-azido-5-fluoro and 6-amino-5-fluoro uridine derivatives exhibited potential for further investigations.


  • Organizational Affiliation
    • Center for Molecular Design and Preformulations and Division of Cellular and Molecular Biology, Toronto General Research Institute, Toronto General Hospital, Toronto, Ontario M5G 2C4, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotidine 5'-phosphate decarboxylase
A, B, C, D
342Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: gi|9310996PF10_0225
EC: 4.1.1.23
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FNU
Query on FNU

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
K [auth C],
M [auth D]
6-amino-5-fluorouridine 5'-(dihydrogen phosphate)
C9 H13 F N3 O9 P
OLBMCLUPWOAIRA-UMMCILCDSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
J [auth B],
L [auth C]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
H [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.592α = 90
b = 82.905β = 90.93
c = 91.73γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
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: 2012-04-18
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description