Canmetcon
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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 (5'->5')-dinucleotides. These are dinucleotides where the two bases are connected via a (5'->5')-phosphodiester linkage.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
Class(5'->5')-dinucleotides
Sub ClassNot Available
Direct Parent(5'->5')-dinucleotides
Alternative Parents
Substituents
  • (5'->5')-dinucleotide
  • Purine nucleotide sugar
  • Purine ribonucleoside 2',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Nicotinamide-nucleotide
  • Pyridine nucleotide
  • Pentose phosphate
  • Pentose-5-phosphate
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Imidazopyrimidine
  • Nicotinamide
  • Purine
  • Aminopyrimidine
  • Monoalkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Alkyl phosphate
  • Phosphoric acid ester
  • Pyridinium
  • Pyridine
  • Imidolactam
  • Imidazole
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Azole
  • Secondary alcohol
  • Carboximidic acid derivative
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Carboximidic acid
  • Primary amine
  • Hydrocarbon derivative
  • Alcohol
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxide
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic 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 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).