3MI2

Crystal structure of human orotidine-5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase.

Meza-Avina, M.E.Wei, L.Liu, Y.Poduch, E.Bello, A.M.Mishra, R.K.Pai, E.F.Kotra, L.P.

(2010) Bioorg Med Chem 18: 4032-4041

  • DOI: 10.1016/j.bmc.2010.04.017
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In recent years, orotidine-5'-monophosphate decarboxylase (ODCase) has gained renewed attention as a drug target. As a part of continuing efforts to design novel inhibitors of ODCase, we undertook a comprehensive study of potent, structurally diverse ...

    In recent years, orotidine-5'-monophosphate decarboxylase (ODCase) has gained renewed attention as a drug target. As a part of continuing efforts to design novel inhibitors of ODCase, we undertook a comprehensive study of potent, structurally diverse ligands of ODCase and analyzed their structural interactions in the active site of ODCase. These ligands comprise of pyrazole or pyrimidine nucleotides including the mononucleotide derivatives of pyrazofurin, barbiturate ribonucleoside, and 5-cyanouridine, as well as, in a computational approach, 1,4-dihydropyridine-based non-nucleoside inhibitors such as nifedipine and nimodipine. All these ligands bind in the active site of ODCase exhibiting distinct interactions paving the way to design novel inhibitors against this interesting enzyme. We propose an empirical model for the ligand structure for rational modifications in new drug design and potentially new lead structures.


    Organizational Affiliation

    Division of Cell & Molecular Biology, University Health Network, Toronto, ON, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uridine 5'-monophosphate synthase
A, B
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
PFU
Query on PFU

Download CCD File 
A, B
(1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol
C9 H14 N3 O9 P
CUHDHRMGDRLFLH-FLLFQEBCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A,BL-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFUKi:  17   nM  BindingDB
PFUKi:  25.100000381469727   nM  Binding MOAD
PFUKi :  17   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.485α = 90
b = 62.109β = 111.45
c = 70.499γ = 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: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary