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Orotic acid (YMDB00405)

Identification
YMDB IDYMDB00405
NameOrotic acid
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionOrotic acid, also known as orotate or orotsaeure, 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. Orotic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Orotic acid exists in all living species, ranging from bacteria to humans. Orotic acid is a potentially toxic compound.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • 1,2,3,6-Tetrahydro-2,6-dioxo-4-pyrimidecarboxylic acid
  • 2,6-dihydroxy-4-pyrimidinecarboxylic acid
  • 2,6-Dihydroxypyrimidine-4-carboxylic acid
  • 2,6-Dioxo-1,2,3,6-tetrahydro-pyrimidine-4-carboxylic acid
  • 6-Carboxy-2,4-dihydroxypyrimidine
  • 6-Carboxyuracil
  • 6-Uracilcarboxylic acid
  • Animal galactose factor
  • Lactinium
  • ORO
  • Orodin
  • Oropur
  • Orotate
  • Orotic acid
  • Orotonin
  • Orotonsan
  • Oroturic
  • Orotyl
  • uracil-6-carboxylate
  • Uracil-6-carboxylic acid
  • Vitamin B13
  • Whey factor
  • Orotsaeure
  • 1,2,3,6-Tetrahydro-2,6-dioxo-4-pyrimidinecarboxylic acid
  • 1,2,3,6-Tetrahydro-2,6-dioxopyrimidin-4-carbonsaeure
  • 2,6-Dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
  • Acide orotique
  • Acido orotico
  • Acidum oroticum
  • Molkensaeure
  • Orotsaure
  • Uracil-6-carbosaeure
  • Zinc orotate
  • Orotate, zinc
  • Acid, orotic
  • Orotate, potassium
  • Potassium orotate
  • Orotate, sodium
  • Sodium orotate
CAS number65-86-1
WeightAverage: 156.0963
Monoisotopic: 156.017106626
InChI KeyPXQPEWDEAKTCGB-UHFFFAOYSA-N
InChIInChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
IUPAC Name2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
Traditional IUPAC Nameorotic acid
Chemical FormulaC5H4N2O4
SMILES[H]OC(=O)C1=C([H])C(=O)N([H])C(=O)N1[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 point345.5 °C
Experimental Properties
PropertyValueReference
Water Solubility1.82 mg/mL at 18 oC [YALKOWSKY,SH & HE,Y (2003)]PhysProp
LogP-0.83 [SANGSTER (1994)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility12.8 g/LALOGPS
logP0.52ALOGPS
logP-1.2ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)2.83ChemAxon
pKa (Strongest Basic)-6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area95.5 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.27 m³·mol⁻¹ChemAxon
Polarizability12.46 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
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 pyrophosphate → Pyrophosphate + Orotidylic acid
4,5-Dihydroorotic acid + Ubiquinone Q1 → QH(2) + Orotic acid
KEGG Reactions
Ubiquinone-6 + L-Dihydroorotic acid → Ubiquinol-6 + Orotic acid
L-Dihydroorotic acid + oxygen → Orotic acid + Hydrogen peroxide
Fumaric acid + L-Dihydroorotic acid → Orotic acid + Succinic acid
Pyrophosphate + Orotidylic acid ↔ Orotic acid + Phosphoribosyl pyrophosphate
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0udi-1982000000-b20f2ec9a2f1acc84ae1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0zfr-2693000000-07bf11b5177412647d9bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1982000000-b20f2ec9a2f1acc84ae1JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0zfr-2693000000-07bf11b5177412647d9bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-1972000000-c04fb7381d3ca07c9b0aJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-06ri-6900000000-4ba5fde1f8f62c4a2ba2JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-0229-9850000000-8164142820eb5162e753JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)splash10-03di-0900000000-81d73aed73c250fff3aeJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)splash10-0006-9300000000-ecb08d1854a2789480d1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)splash10-0006-9100000000-15748a4c13636c42f4f9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-03di-0900000000-1b7abf52e4a01cb85541JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , negativesplash10-03di-0900000000-1b7abf52e4a01cb85541JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , negativesplash10-03di-0900000000-3dff3caa5c10aff8ce46JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-02ti-4900000000-6fd6312d81f94faaaf11JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-02ti-4900000000-6fd6312d81f94faaaf11JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0900000000-d7bbee7f2dc7bb0c6a83JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03dl-7900000000-303fe3e06e98f518a2eeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-b2c02975bbba65c2f1c6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0900000000-d7bbee7f2dc7bb0c6a83JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-03dl-7900000000-303fe3e06e98f518a2eeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-b2c02975bbba65c2f1c6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0bt9-0900000000-1ad59feda583f2247b21JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-0d0d27215e9f39a2a15bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9100000000-918a38777f5d4e049697JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0bt9-0900000000-1ad59feda583f2247b21JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-2900000000-0d0d27215e9f39a2a15bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9100000000-918a38777f5d4e049697JSpectraViewer
MSMass Spectrum (Electron Ionization)splash10-066r-9300000000-e5c3ef3304f93a38628cJSpectraViewer | MoNA
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableJSpectraViewer
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
  • Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). "Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations." Mol Biol Cell 21:198-211.19889834
Synthesis Reference:Mitchell, Herschel K.; Nyc, Joseph F. Intermediates in the synthesis of orotic acid from oxalacetic ester and urea. Journal of the American Chemical Society (1947), 69 674-7.
External Links:
ResourceLink
CHEBI ID16742
HMDB IDHMDB00226
Pubchem Compound ID967
Kegg IDC00295
ChemSpider ID942
FOODB IDFDB031072
WikipediaOrotic_acid
BioCyc IDOROTATE

Enzymes

Protein Details
1. Orotate phosphoribosyltransferase 1
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.
Protein Details
2. Orotate phosphoribosyltransferase 2
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.
Protein Details
3. Dihydroorotate dehydrogenase
General function:
Involved in catalytic activity
Specific function:
In the de novo pyrimidine biosynthesic pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate and the reduction of fumarate to succinate. Does not use oxaloacetate and NAD or NADP as electron acceptors
Gene Name:
URA1
Uniprot ID:
P28272
Molecular weight:
34800.60156
Reactions
(S)-dihydroorotate + O(2) → orotate + H(2)O(2).
(S)-dihydroorotate + a quinone → orotate + a quinol