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Record Information
Version4.0
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-10-23 18:22:38 UTC
HMDB IDHMDB0000788
Secondary Accession Numbers
  • HMDB00788
Metabolite Identification
Common NameOrotidine
DescriptionOrotidine is a nucleoside formed by attaching orotic acid to a ribose ring via a β-N1-glycosidic bond. It is found in bacteria, fungi and plants. In humans, orotidine occurs as its 5'-phosphate (orotidylic acid), which is an intermediate in pyrimidine nucleotide biosynthesis (cytidine and uridine) that are found in nucleic acids. Ornitidine itself is not a component of nucleic acid. Large amounts of ornitidine are excreted in the urine of cancer patients treated with 6-azauridine. (Wikipedia).
Structure
Thumb
Synonyms
ValueSource
3-Ribofuranosylorotic acidChEBI
6-CarboxyuridineChEBI
3-RibofuranosylorotateGenerator
Orotic acid ribosideHMDB
Orotidine, ammonium saltMeSH
Chemical FormulaC10H12N2O8
Average Molecular Weight288.2109
Monoisotopic Molecular Weight288.05936537
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
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(=O)NC(=O)C=C1C(O)=O
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
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleosides
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
  • Oxolane
  • Secondary alcohol
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • 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
Ontology
Disposition

Biological Location:

  Subcellular:

  Biofluid and excreta:

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point> 400 °CNot Available
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
Polarizability24.99 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05i3-9230000000-e2c457e981d3f20213c6View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positivesplash10-03ei-4340390000-f308e272596bbf4876aaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-0f92-6790000000-22b02fcae382ac45192aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4r-0940000000-ae1aee48fbe832808af5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4r-1920000000-8d5291c4fd7f7d30f0bbView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0aou-8900000000-b3e3dadd94fb667cbb00View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052o-3970000000-a100d1c804d27c0b6e97View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bt9-0910000000-1a9d30040efa9eecd74dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-01ox-9600000000-001a262ee2894d294d1cView in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
No entries found
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified149.0 +/- 13.0 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified1.12 +/- 0.20 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB012085
KNApSAcK IDNot Available
Chemspider ID83729
KEGG Compound IDC01103
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkOrotidine
METLIN ID5754
PubChem Compound92751
PDB IDNot Available
ChEBI ID25722
References
Synthesis ReferenceCurra, William V.; Angle, Robert B. Synthesis of orotidine. Tetrahedron Letters (1963), (8), 533-5.
Material Safety Data Sheet (MSDS)Download (PDF)
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 ]