3G3M

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-iodo-UMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


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: 10.1021/jm801224t
  • Structures With Same Primary Citation

  • 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-fluor ...

    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: 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5FU
Query on 5FU

Download CCD File 
A
5-FLUORO-URIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O9 P
RNBMPPYRHNWTMA-UAKXSSHOSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5FUKi:  98000   nM  BindingDB
5FUKi :  1100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.28α = 90
b = 116.558β = 90
c = 62.113γ = 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: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance