4HKP

Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N3-oxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 

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
  • Primary Citation of Related Structures:  4HIB

  • 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 sapiensGene Names: UMPS
EC: 2.4.2.10, 4.1.1.23
Find proteins for P11172 (Homo sapiens)
Go to Gene View: UMPS
Go to UniProtKB:  P11172
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
16B
Query on 16B

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

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TKW
Query on TKW

Download SDF File 
Download CCD File 
A, B
5-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
QONOHPMEMVHOPP-UAKXSSHOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
16BKi: 28300 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.290α = 90.00
b = 61.775β = 112.90
c = 70.523γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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