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 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1021/jm301176r
  • Primary Citation of Related Structures:  
    4HIB, 4HKP

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
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)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens)
Explore P11172 
Go to UniProtKB:  P11172
PHAROS:  P11172
GTEx:  ENSG00000114491 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11172
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
16B
Query on 16B

Download Ideal Coordinates CCD File 
G [auth A]N-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
DYOUVDKCXLKHKY-XVFCMESISA-N
TKW
Query on TKW

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
5-hydroxycytidine 5'-(dihydrogen phosphate)
C9 H14 N3 O9 P
QONOHPMEMVHOPP-UAKXSSHOSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
H [auth B]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
16B PDBBind:  4HKP Ki: 2.83e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.29α = 90
b = 61.775β = 112.9
c = 70.523γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references