Orotidylic acid (PAMDB000090)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000090
Identification
Name: Orotidylic acid
Description:Orotidylic 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 Pseudomonas aeruginosa, the enzyme UMP synthase converts OMP into uridine 5'- monophosphate. If UMP synthase is defective, orotic aciduria can result. (Wikipedia)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylate
  • 1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-D-ribofuranosyl)-4-Pyrimidinecarboxylic acid
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-4-pyrimidinecarboxylate
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-4-pyrimidinecarboxylic acid
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-4-pyrimidinecarboxylate
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-4-pyrimidinecarboxylic acid
  • 1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylate
  • 1,2,3,6-Tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylic acid
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-4-pyrimidinecarboxylate
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-4-pyrimidinecarboxylic acid
  • 2,6-dioxo-3-(5-O-phosphono-b-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-dioxo-3-(5-O-phosphono-b-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-dioxo-3-(5-O-phosphono-b-delta-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-dioxo-3-(5-O-phosphono-b-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-Dioxo-3-(5-O-phosphono-beta-D-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-Dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-dioxo-3-(5-O-phosphono-β-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-dioxo-3-(5-O-phosphono-β-D-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylate
  • 2,6-dioxo-3-(5-O-phosphono-β-δ-Ribofuranosyl)-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • 5'-(Dihydrogen phosphate) 6-carboxy-uridine
  • 5'-(Dihydrogen phosphate) Orotidine
  • 5'-(Dihydrogen phosphoric acid) 6-carboxy-uridine
  • 5'-(Dihydrogen phosphoric acid) orotidine
  • 5'-OMP
  • 5'-Phosphate Orotidine
  • 5'-Phosphoric acid orotidine
  • 5-(Dihydrogen phosphate)orotidine
  • 5-(Dihydrogen phosphoric acid)orotidine
  • 6-Carboxy-5'-uridylate
  • 6-Carboxy-5'-uridylic acid
  • Ometoprim
  • OMP
  • Omp (nucleotide)
  • Orotidine 5'-(dihydrogen phosphate)
  • Orotidine 5'-(dihydrogen phosphoric acid)
  • Orotidine 5'-monophosphate
  • Orotidine 5'-monophosphoric acid
  • Orotidine 5'-phosphate
  • Orotidine 5'-phosphoric acid
  • Orotidine monophosphate
  • Orotidine monophosphoric acid
  • Orotidine-5'-phosphate
  • Orotidine-5'-phosphoric acid
  • Orotidine5'P
  • Orotidylate
  • Orotidylic acid
Chemical Formula: C10H13N2O11P
Average Molecular Weight: 368.1908
Monoisotopic Molecular Weight: 368.02569578
InChI Key: KYOBSHFOBAOFBF-XVFCMESISA-N
InChI: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
CAS number: 2149-82-8
IUPAC Name:3-[(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 IUPAC Name: 6-carboxy-5'-uridylic acid
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
Chemical Taxonomy
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.
Kingdom Organic compounds
Super ClassNucleosides, nucleotides, and analogues
Class Pyrimidine nucleotides
Sub ClassPyrimidine ribonucleotides
Direct Parent Pyrimidine 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 Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueSource
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
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Hydrogen ion + Orotidylic acid <> Carbon dioxide + Uridine 5'-monophosphate
Orotidylic acid + Pyrophosphate <> Orotic acid + Phosphoribosyl pyrophosphate
Orotidylic acid <> Uridine 5'-monophosphate + Carbon dioxide
Orotic acid + Phosphoribosyl pyrophosphate > Pyrophosphate + Orotidylic acid
Pathways:
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
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • 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. Pubmed: 19212411
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Ueda, 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, Nuc
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID15842
HMDB IDHMDB00218
Pubchem Compound ID160617
Kegg IDC01103
ChemSpider ID141140
WikipediaOrotidylic acid
BioCyc IDOROTIDINE-5-PHOSPHATE
EcoCyc IDOROTIDINE-5-PHOSPHATE
Ligand ExpoOMP