4HIB

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N4-OH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel cytidine-based orotidine-5'-monophosphate decarboxylase inhibitors with an unusual twist.

Purohit, M.K.Poduch, E.Wei, L.W.Crandall, I.E.To, T.Kain, K.C.Pai, E.F.Kotra, L.P.

(2012) J Med Chem 55: 9988-9997

  • DOI: 10.1021/jm301176r
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Orotidine-5'-monophosphate decarboxylase (ODCase) is an interesting enzyme with an unusual catalytic activity and a potential drug target in Plasmodium falciparum, which causes malaria. ODCase has been shown to exhibit unusual and interesting interac ...

    Orotidine-5'-monophosphate decarboxylase (ODCase) is an interesting enzyme with an unusual catalytic activity and a potential drug target in Plasmodium falciparum, which causes malaria. ODCase has been shown to exhibit unusual and interesting interactions with a variety of nucleotide ligands. Cytidine-5'-monophosphate (CMP) is a poor ligand of ODCase, and CMP binds to the active site of ODCase with an unusual orientation and conformation. We designed N3- and N4-modified CMP derivatives as novel ligands to ODCase. These novel CMP derivatives and their corresponding nucleosides were evaluated against Plasmodium falciparum ODCase and parasitic cultures, respectively. These derivatives exhibited improved inhibition of the enzyme catalytic activity, displayed interesting binding conformations and unusual molecular rearrangements of the ligands. These findings with the modified CMP nucleotides underscored the potential of transformation of poor ligands to ODCase into novel inhibitors of this drug target.


    Organizational Affiliation

    Center for Molecular Design and Preformulations, Toronto General Research Institute, University Health Network, Toronto, Ontario M5G 1L7, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine 5'-monophosphate synthase
A, B
312Homo sapiensMutation(s): 0 
Gene Names: UMPSOK/SW-cl.21
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16B
Query on 16B

Download CCD File 
A, B
N-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
DYOUVDKCXLKHKY-XVFCMESISA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.78α = 90
b = 61.64β = 112.08
c = 71.37γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Macromoleculardata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references