You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:02:17 UTC
HMDB IDHMDB00218
Secondary Accession NumbersNone
Metabolite Identification
Common NameOrotidylic acid
DescriptionOrotidylic acid (OMP), is a pyrimidine nucleotide which is the last intermediate in the biosynthesis of uridine monophosphate. Decarboxylation by Orotidylate decarboxylase affords Uridine 5'-phosphate which is the route to Uridine and its derivatives de novo and consequently one of the most important processes in nucleic acid synthesis (Dictionary of Organic Compounds). In humans, the enzyme UMP synthase converts OMP into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result. (Wikipedia).
Structure
Thumb
Synonyms
ValueSource
6-Carboxy-5'-uridylic acidChEBI
Orotidine 5'-(dihydrogen phosphate)ChEBI
Orotidylic acidChEBI
6-Carboxy-5'-uridylateGenerator
Orotidine 5'-phosphoric acidGenerator
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 monophosphateHMDB
Orotidine-5'-phosphateHMDB
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 KeyInChIKey=KYOBSHFOBAOFBF-XVFCMESISA-N
Chemical Taxonomy
DescriptionThis compound 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
  • N-glycosyl compound
  • Glycosyl compound
  • Monosaccharide phosphate
  • Pyrimidine-6-carboxylic acid or derivatives
  • Pyrimidine-6-carboxylic acid
  • Hydropyrimidine carboxylic acid derivative
  • Hydroxypyrimidine
  • Monoalkyl phosphate
  • Pyrimidone
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Oxolane
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Cytoplasm
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 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity70.74 m3·mol-1ChemAxon
Polarizability29.7 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0914000000-3337770bad1b3ba8486cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-1911000000-f94acf2aa5da3364c517View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-5900000000-81a1aba75871162fc05bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0axv-8917000000-d1de3bc4514e88dd288cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9701000000-13540f203bff602cb8f5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-2bf7c464e9b79ae5c6a9View in MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Prostate Tissue
Tissue Location
  • Prostate
Pathways
NameSMPDB LinkKEGG Link
3-Phosphoglycerate dehydrogenase deficiencySMP00721Not Available
Beta Ureidopropionase DeficiencySMP00172Not Available
Dihydropyrimidinase DeficiencySMP00178Not Available
Dihydropyrimidine Dehydrogenase Deficiency (DHPD)SMP00179Not Available
Dimethylglycine Dehydrogenase DeficiencySMP00242Not Available
Dimethylglycine Dehydrogenase DeficiencySMP00484Not Available
Glycine and Serine MetabolismSMP00004map00260
Hyperglycinemia, non-ketoticSMP00485Not Available
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)SMP00202Not Available
Non Ketotic HyperglycinemiaSMP00223Not Available
Pyrimidine MetabolismSMP00046map00240
SarcosinemiaSMP00244Not Available
UMP Synthase Deiciency (Orotic Aciduria)SMP00219Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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. [19212411 ]
Associated OMIM IDs
DrugBank IDDB02957
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB012321
KNApSAcK IDNot Available
Chemspider ID141140
KEGG Compound IDC01103
BioCyc IDOROTIDINE-5-PHOSPHATE
BiGG ID36813
Wikipedia LinkOrotidylic acid
NuGOwiki LinkHMDB00218
Metagene LinkHMDB00218
METLIN ID5228
PubChem Compound160617
PDB IDOMP
ChEBI ID15842
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. 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. [19212411 ]
  2. Traut TW: Uridine-5'-phosphate synthase: evidence for substrate cycling involving this bifunctional protein. Arch Biochem Biophys. 1989 Jan;268(1):108-15. [2912371 ]

Enzymes

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