3MO7

Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 2'-fluoro-6-iodo-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel interactions of fluorinated nucleotide derivatives targeting orotidine 5'-monophosphate decarboxylase.

Lewis, M.Meza-Avina, M.E.Wei, L.Crandall, I.E.Bello, A.M.Poduch, E.Liu, Y.Paige, C.J.Kain, K.C.Pai, E.F.Kotra, L.P.

(2011) J Med Chem 54: 2891-2901

  • DOI: 10.1021/jm101642g
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fluorinated nucleosides and nucleotides are of considerable interest to medicinal chemists because of their antiviral, anticancer, and other biological activities. However, their direct interactions at target binding sites are not well understood. A ...

    Fluorinated nucleosides and nucleotides are of considerable interest to medicinal chemists because of their antiviral, anticancer, and other biological activities. However, their direct interactions at target binding sites are not well understood. A new class of 2'-deoxy-2'-fluoro-C6-substituted uridine and UMP derivatives were synthesized and evaluated as inhibitors of orotidine 5'-monophosphate decarboxylase (ODCase or OMPDCase). These compounds were synthesized from the key intermediate, fully protected 2'-deoxy-2'-fluorouridine. Among the synthesized compounds, 2'-deoxy-2'-fluoro-6-iodo-UMP covalently inhibited human ODCase with a second-order rate constant of 0.62 ± 0.02 M(-1) s(-1). Interestingly, the 6-cyano-2'-fluoro derivative covalently interacted with ODCase defying the conventional thinking, where its ribosyl derivative undergoes transformation into BMP by ODCase. This confirms that the 2'-fluoro moiety influences the chemistry at the C6 position of the nucleotides and thus interactions in the active site of ODCase. Molecular interactions of the 2'-fluorinated nucleotides are compared to those with the 3'-fluorinated nucleotides bound to the corresponding target enzyme, and the carbohydrate moieties were shown to bind in different conformations.


    Organizational Affiliation

    Center for Molecular Design and Preformulations and Division of Cellular and Molecular Biology, Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine 5'-monophosphate synthase
A
279Homo sapiensMutation(s): 0 
Gene Names: gi|13960142OK/SW-cl.21UMPS
EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
Find proteins for P11172 (Homo sapiens)
Go to UniProtKB:  P11172
NIH Common Fund Data Resources
PHAROS  P11172
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UFT
Query on UFT

Download CCD File 
A
2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
C9 H12 F N2 O8 P
RTGGYPQTXNSBPD-XVFCMESISA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.499α = 90
b = 116.035β = 90
c = 62.103γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance