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: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 

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
  • Primary Citation of Related Structures:  

  • 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: UMPS
Find proteins for P11172 (Homo sapiens)
Go to Gene View: UMPS
Go to UniProtKB:  P11172
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5FU
Query on 5FU

Download SDF File 
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
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5FUKi: 98000 nM (100) BINDINGDB
5FUKi: 1100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.159 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 78.280α = 90.00
b = 116.558β = 90.00
c = 62.113γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MxDCdata collection
MOLREPphasing
Cootmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance