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Showing metabocard for Orotidylic acid (HMDB0000218)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-05-12 18:46:58 UTC
HMDB IDHMDB0000218
Secondary Accession Numbers
  • HMDB00218
Metabolite Identification
Common NameOrotidylic acid
DescriptionOrotidylic acid, also known as orotidylate or 5'-OMP, belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. Orotidylic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Orotidylic acid exists in all living species, ranging from bacteria to humans. guanidoacetic acid and orotidylic acid can be biosynthesized from glycine and L-arginine; which is catalyzed by the enzyme glycine amidinotransferase, mitochondrial. In humans, orotidylic acid is involved in the metabolic disorder called the dimethylglycine dehydrogenase deficiency pathway. Outside of the human body, Orotidylic acid has been detected, but not quantified in, several different foods, such as parsley, common persimmons, other bread, oriental wheats, and custard apples. This could make orotidylic acid a potential biomarker for the consumption of these foods. A pyrimidine ribonucleoside 5'-monophosphate having 6-carboxyuracil as the nucleobase.
Structure
Data?1589309216
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
ValueSource
6-Carboxy-5'-uridylic acidChEBI
Orotidine 5'-(dihydrogen phosphate)ChEBI
6-Carboxy-5'-uridylateGenerator
Orotidine 5'-(dihydrogen phosphoric acid)Generator
OrotidylateGenerator
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-pyrimidinecarboxylateHMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-pyrimidinecarboxylic acidHMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-pyrimidinecarboxylateHMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-pyrimidinecarboxylic acidHMDB
2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acidHMDB
2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acidHMDB
5'-(Dihydrogen phosphate) 6-carboxy-uridineHMDB
5'-(Dihydrogen phosphate) orotidineHMDB
5'-OMPHMDB
5'-Phosphate orotidineHMDB
5-(Dihydrogen phosphate)orotidineHMDB
OmetoprimHMDB
OMPHMDB
Omp (nucleotide)HMDB
Orotidine 5'-monophosphateHMDB
Orotidine 5'-phosphateHMDB
Orotidine monophosphateHMDB
Orotidine-5'-phosphateHMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-4-pyrimidinecarboxylic acidHMDB
1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-D-ribofuranosyl)-4-pyrimidinecarboxylic acidHMDB
5’-OMPHMDB
Orotidine 5’-monophosphateHMDB
Orotidylic acidHMDB
Chemical FormulaC10H13N2O11P
Average Molecular Weight368.1908
Monoisotopic Molecular Weight368.02569578
IUPAC Name3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-2-yl]-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
Traditional Name6-carboxy-5'-uridylic acid
CAS Registry Number2149-82-8
SMILES
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)N1C(=O)NC(=O)C=C1C(O)=O
InChI Identifier
InChI=1S/C10H13N2O11P/c13-5-1-3(9(16)17)12(10(18)11-5)8-7(15)6(14)4(23-8)2-22-24(19,20)21/h1,4,6-8,14-15H,2H2,(H,16,17)(H,11,13,18)(H2,19,20,21)/t4-,6-,7-,8-/m1/s1
InChI KeyKYOBSHFOBAOFBF-XVFCMESISA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct ParentPyrimidine ribonucleoside monophosphates
Alternative Parents
Substituents
  • Pyrimidine ribonucleoside monophosphate
  • Pentose-5-phosphate
  • Pentose phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Pyrimidine-6-carboxylic acid or derivatives
  • Pyrimidine-6-carboxylic acid
  • Hydropyrimidine carboxylic acid derivative
  • Monoalkyl phosphate
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Alkyl phosphate
  • Phosphoric acid ester
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Secondary alcohol
  • Urea
  • Lactam
  • 1,2-diol
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Oxacycle
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic nitrogen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility8.61 g/LALOGPS
logP-1.7ALOGPS
logP-2.9ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.21ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count10ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area203.16 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity70.74 m³·mol⁻¹ChemAxon
Polarizability29.65 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9512000000-a3f8062edabfeda1eaa8Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0002-9221230000-0c722324f49458fdfb65Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0914000000-3337770bad1b3ba8486cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-1911000000-f94acf2aa5da3364c517Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-5900000000-81a1aba75871162fc05bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0axv-8917000000-d1de3bc4514e88dd288cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9701000000-13540f203bff602cb8f5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-2bf7c464e9b79ae5c6a9Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Prostate Tissue
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Prostate TissueDetected and Quantified0.5 (0.0-1.0) umol/g tissueAdult (>18 years old)Both
Prostate Cancer		 details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDDB02957
Phenol Explorer Compound IDNot Available
FooDB IDFDB031073
KNApSAcK IDC00007583
Chemspider ID141140
KEGG Compound IDC01103
BioCyc IDOROTIDINE-5-PHOSPHATE
BiGG ID36813
Wikipedia LinkOrotidine 5'-monophosphate
METLIN ID5228
PubChem Compound160617
PDB IDNot Available
ChEBI ID15842
Food Biomarker OntologyNot Available
VMH IDOROT5P
References
Synthesis ReferenceUeda, Tohru; Yamamoto, Miyako; Yamane, Akira; Imazawa, Masaoki; Inoue, Hideo. Nucleosides and nucleotides. XXIII. Conversion of uridine nucleotides to the 6-cyano derivatives: synthesis of orotidylic acid. Journal of Carbohydrates, Nucleosides, Nucleotides (1978), 5(3), 261-71.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Traut TW: Uridine-5'-phosphate synthase: evidence for substrate cycling involving this bifunctional protein. Arch Biochem Biophys. 1989 Jan;268(1):108-15. [PubMed:2912371 ]
  2. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]

Enzymes

Enzyme Details
1. Uridine 5'-monophosphate synthase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
UMPS
Uniprot ID:
P11172
Molecular weight:
52221.075
Reactions
Orotidylic acid + Pyrophosphate → Orotic acid + Phosphoribosyl pyrophosphatedetails
Orotidylic acid → Uridine 5'-monophosphate + CO(2)details
Orotidylic acid → Uridine 5'-monophosphate + Carbon dioxidedetails