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Identification
YMDB IDYMDB00025
NameOrotidylic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionOrotidylic acid (orotidine 5'-monophosphate) is the last intermediate in the uridine-5'-phosphate biosynthesis pathway. Uridine-5'-phosphate (UMP) is a pyrimidine used for the de novo biosynthesis of pyrimidine nucleotides. [Biocyc PWY-5686]
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 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
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
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 IDFDB031073
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).