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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-16 18:04:13 UTC
NP-MRD IDNP0000088
Secondary Accession NumbersNone
Natural Product Identification
Common NameOrotidine
DescriptionOrotidine is a nucleoside formed by attaching orotic acid to a ribose ring via a beta-N1-glycosidic bond. It is a water-soluble solid. Orotidine is found in bacteria, fungi, plants, and animals. In humans, orotidine occurs as its 5'-phosphate (orotidylic acid), which is an intermediate in the biosynthesis of pyrimidine nucleosides (cytidine and uridine) that are found in nucleic acids (as the nucleotides containing the bases cytosine and uracil). Orotidine itself is not a component of nucleic acid. Orotidine monophosphate (OMP) is converted to uridine monophosphate by OMP decarboxylase, which is inhibited by mononucleotide precursors. Large amounts of orotidine are excreted in the urine of cancer patients treated with 6-azauridine, which is one such inhibitor, indicating that the subject has increased DNA synthesis due to cancer. Orotidine was first isolated from a mutant strain of the fungus Neurospora by A. Michael Michelson, William Drell, and Herschel K. Mitchell (PMID: 14853953 ).
Structure
Data?1628564077
Synonyms
ValueSource
3-Ribofuranosylorotic acidChEBI
6-CarboxyuridineChEBI
3-RibofuranosylorotateGenerator
Orotic acid ribosideHMDB
Orotidine, ammonium saltHMDB
Chemical FormulaC10H12N2O8
Average Mass288.2109 Da
Monoisotopic Mass288.05937 Da
IUPAC Name3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
Traditional Nameorotidine
CAS Registry Number314-50-1
SMILES
[H]OC(=O)C1=C([H])C(=O)N([H])C(=O)N1[C@]1([H])O[C@]([H])(C([H])([H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]
InChI Identifier
InChI=1S/C10H12N2O8/c13-2-4-6(15)7(16)8(20-4)12-3(9(17)18)1-5(14)11-10(12)19/h1,4,6-8,13,15-16H,2H2,(H,17,18)(H,11,14,19)/t4-,6-,7-,8-/m1/s1
InChI KeyFKCRAVPPBFWEJD-XVFCMESISA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)V.dorna832021-09-03View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)V.dorna832021-09-03View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)Varshavi.d262021-08-08View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Phaseolus vulgarisKNApSAcK Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Hydropyrimidine carboxylic acid derivative
  • Pyrimidine-6-carboxylic acid
  • Pyrimidine-6-carboxylic acid or derivatives
  • Hydroxypyrimidine
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Azacycle
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organooxygen compound
  • Organic oxide
  • Primary alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 400 °Chttps://en.wikipedia.org/wiki/Orotidine
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility44.7 g/LALOGPS
logP-2ALOGPS
logP-2.8ChemAxon
logS-0.81ALOGPS
pKa (Strongest Acidic)2.86ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area156.63 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity59.87 m³·mol⁻¹ChemAxon
Polarizability25 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000788
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB012085
KNApSAcK IDC00054976
Chemspider ID83729
KEGG Compound IDC01103
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkOrotidine
METLIN ID5754
PubChem Compound92751
PDB IDNot Available
ChEBI ID25722
Good Scents IDNot Available
References
General References
  1. Arranz JA, Riudor E, Rodes M, Roig M, Climent C, Rubio V, Sentis M, Burlina A: Optimization of allopurinol challenge: sample purification, protein intake control, and the use of orotidine response as a discriminative variable improve performance of the test for diagnosing ornithine carbamoyltransferase deficiency. Clin Chem. 1999 Jul;45(7):995-1001. [PubMed:10388475 ]
  2. Harris ML, Oberholzer VG: Conditions affecting the colorimetry of orotic acid and orotidine in urine. Clin Chem. 1980 Mar;26(3):473-9. [PubMed:7363468 ]
  3. van Kuilenburg AB, van Lenthe H, Loffler M, van Gennip AH: Analysis of pyrimidine synthesis "de novo" intermediates in urine and dried urine filter- paper strips with HPLC-electrospray tandem mass spectrometry. Clin Chem. 2004 Nov;50(11):2117-24. Epub 2004 Sep 16. [PubMed:15375016 ]
  4. MICHELSON AM, DRELL W, MITCHELL HK: A new ribose nucleoside from Neurospora; "orotidine". Proc Natl Acad Sci U S A. 1951 Jul;37(7):396-9. doi: 10.1073/pnas.37.7.396. [PubMed:14853953 ]
  5. Matsuo Y, Nishino K, Mizuno K, Akihiro T, Toda T, Matsuo Y, Kaino T, Kawamukai M: Polypeptone induces dramatic cell lysis in ura4 deletion mutants of fission yeast. PLoS One. 2013;8(3):e59887. doi: 10.1371/journal.pone.0059887. Epub 2013 Mar 21. [PubMed:23555823 ]