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Identification
YMDB IDYMDB00025
NameOrotidylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionOrotidylic acid, also known as 5'-OMP or orotidylate, belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring. 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. Within yeast, orotidylic acid participates in a number of enzymatic reactions. In particular, orotidylic acid can be biosynthesized from orotic acid and phosphoribosyl pyrophosphate; which is catalyzed by the enzyme orotate phosphoribosyltransferase. In addition, orotidylic acid can be converted into uridine 5'-monophosphate through the action of the enzyme orotidine-5'-phosphate decarboxylase. In yeast, orotidylic acid is involved in the metabolic pathway called the pyrimidine metabolism pathway.
Structure
Thumb
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-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylate
  • 1,2,3,6-tetrahydro-2,6-dioxo-3-(5-O-phosphono-beta-delta-ribofuranosyl)-4-Pyrimidinecarboxylic acid
  • 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-carboxylic acid
  • 5-(Dihydrogen phosphate)orotidine
  • 5'-(dihydrogen phosphate) 6-carboxy-uridine
  • 5'-(dihydrogen phosphate) Orotidine
  • 5'-OMP
  • 5'-phosphate 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'-phosphate
  • Orotidine monophosphate
  • orotidine-5'-phosphate
  • Orotidylate
  • Orotidylic acid
CAS number2149-82-8
WeightAverage: 368.1908
Monoisotopic: 368.02569578
InChI KeyKYOBSHFOBAOFBF-XVFCMESISA-N
InChIInChI=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
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 IUPAC Name6-carboxy-5'-uridylic acid
Chemical FormulaC10H13N2O11P
SMILES[H]OC(=O)C1=C([H])C(=O)N([H])C(=O)N1[C@]1([H])O[C@]([H])(C([H])([H])OP(=O)(O[H])O[H])[C@@]([H])(O[H])[C@@]1([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidinecarboxylic acids. These are pyrimidines with a structure containing a carboxyl group attached to the pyrimidine ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidinecarboxylic acids
Alternative Parents
Substituents
  • Pyrimidine-6-carboxylic acid
  • Hydropyrimidine carboxylic acid derivative
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Urea
  • Lactam
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Polarizability29.7 ųChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • cytoplasm
Organoleptic PropertiesNot Available
SMPDB Pathways
Pyrimidine metabolismPW002469 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pyrimidine metabolismec00240 Map00240
SMPDB Reactions
Orotic acid + Phosphoribosyl pyrophosphatePyrophosphate + Orotidylic acid
Orotidylic acid + hydronCarbon dioxide + Uridine 5'-monophosphate
KEGG Reactions
Pyrophosphate + Orotidylic acidOrotic acid + Phosphoribosyl pyrophosphate
hydron + Orotidylic acidCarbon dioxide + Uridine 5'-monophosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9512000000-a3f8062edabfeda1eaa8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0002-9221230000-0c722324f49458fdfb65JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0914000000-3337770bad1b3ba8486cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-1911000000-f94acf2aa5da3364c517JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-5900000000-81a1aba75871162fc05bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0axv-8917000000-d1de3bc4514e88dd288cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-9701000000-13540f203bff602cb8f5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9200000000-2bf7c464e9b79ae5c6a9JSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Victor, J., Greenberg, L. B., Sloan, D. L. (1979). "Studies of the kinetic mechanism of orotate phosphoribosyltransferase from yeast." J Biol Chem 254:2647-2655.218950
  • Gonzalez-Segura, L., Witte, J. F., McClard, R. W., Hurley, T. D. (2007). "Ternary complex formation and induced asymmetry in orotate phosphoribosyltransferase." Biochemistry 46:14075-14086.18020427
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
External Links:
ResourceLink
CHEBI ID15842
HMDB IDHMDB00218
Pubchem Compound ID160617
Kegg IDC01103
ChemSpider ID141140
FOODB IDFDB012321
WikipediaOrotidine_5'-monophosphate
BioCyc IDOROTIDINE-5-PHOSPHATE

Enzymes

General function:
Involved in orotate phosphoribosyltransferase activity
Specific function:
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
Gene Name:
URA5
Uniprot ID:
P13298
Molecular weight:
24664.19922
Reactions
Orotidine 5'-phosphate + diphosphate → orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in orotate phosphoribosyltransferase activity
Specific function:
Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
Gene Name:
URA10
Uniprot ID:
P30402
Molecular weight:
24810.30078
Reactions
Orotidine 5'-phosphate + diphosphate → orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
General function:
Involved in catalytic activity
Specific function:
Orotidine 5'-phosphate = UMP + CO(2)
Gene Name:
URA3
Uniprot ID:
P03962
Molecular weight:
29239.30078
Reactions
Orotidine 5'-phosphate → UMP + CO(2).