3MI2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 

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
  • Also Cited By: 3SEC

  • 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: 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
PFU
Query on PFU

Download SDF File 
Download CCD File 
A, B
(1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol
Pyrazofurin Monophosphate
C9 H14 N3 O9 P
CUHDHRMGDRLFLH-FLLFQEBCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
A, B
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFUKi: 17 nM (100) BINDINGDB
PFUKi: 25.1 nM BINDINGMOAD
PFUKi: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.485α = 90.00
b = 62.109β = 111.45
c = 70.499γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MxDCdata collection
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary