Uracil (PAMDB000126)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000126
Identification
Name: Uracil
Description:Uracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes. In Pseudomonas aeruginosa, uracil catabolism is regulated by the amount of metabolically available nitrogen.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 2,4-Dihydroxypyrimidine
  • 2,4-Dioxopyrimidine
  • 2,4-Pyrimidinediol
  • 2,4-Pyrimidinedione
  • Hybar X
  • Pirod
  • Pyrod
  • Uracil
Chemical Formula: C4H4N2O2
Average Molecular Weight: 112.0868
Monoisotopic Molecular Weight: 112.027277382
InChI Key: ISAKRJDGNUQOIC-UHFFFAOYSA-N
InChI:InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
CAS number: 66-22-8
IUPAC Name:1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name: uracil
SMILES:O=C1NC=CC(=O)N1
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as pyrimidones. These are compounds that contain a pyrimidine ring,which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
Kingdom Organic compounds
Super ClassOrganoheterocyclic compounds
Class Diazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct Parent Pyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Urea
  • Lactam
  • Azacycle
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:0
Melting point: 330 °C
Experimental Properties:
PropertyValueSource
Water Solubility:3.6 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]PhysProp
LogP:-1.07 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility26.5 mg/mLALOGPS
logP-1.2ALOGPS
logP-0.86ChemAxon
logS-0.63ALOGPS
pKa (Strongest Acidic)9.77ChemAxon
pKa (Strongest Basic)-5.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25.97 m3·mol-1ChemAxon
Polarizability9.37 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Hydrogen ion + NADH + Oxygen + Uracil > NAD + Ureidoacrylate peracid
Dihydrouracil + NAD <> Hydrogen ion + NADH + Uracil
Water + Uridine > Ribose + Uracil
Deoxyuridine + Phosphate <> Deoxyribose 1-phosphate + Uracil
Cytosine + Hydrogen ion + Water > Ammonium + Uracil
Phosphoribosyl pyrophosphate + Uracil <> Pyrophosphate + Uridine 5'-monophosphate
Phosphate + Uridine <> Ribose-1-phosphate + Uracil
Cytosine + Water <> Uracil + Ammonia
Uridine + Phosphate <> Uracil + alpha-D-Ribose 1-phosphate + Ribose-1-phosphate
Uracil + FMNH + Oxygen <> Ureidoacrylate peracid + Flavin Mononucleotide
Deoxyuridine + Phosphate <> deoxyribose-1-phosphate + Uracil
D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate
Uracil + Oxygen + FMNH > Hydrogen ion + Ureidoacrylate peracid + Flavin Mononucleotide
Uridine + Water > D-ribose + Uracil
Dihydrouracil + NAD > Uracil + NADH
Uracil + FMNH(2) + Oxygen > Ureidoacrylate peracid + Flavin Mononucleotide + Water
Uridine + Inorganic phosphate > Uracil + Ribose-1-phosphate
Dihydrouracil + NAD + Dihydrothymine <> Uracil + NADH + Hydrogen ion + Thymine
Uracil + FMNH + Oxygen + Thymine <> Ureidoacrylate peracid + Flavin Mononucleotide + (Z)-2-Methyl-ureidoacrylate peracid
Pseudouridine 5'-phosphate + Water > Uracil + D-ribofuranose 5-phosphate + D-ribofuranose 5-phosphate
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0002-5950000000-18425875415ad150c4fcView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-006t-9740000000-e884a4b98e7e9dc75e5fView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-052e-7790000000-026cb6beb5cde6a61b80View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-03di-3900000000-e422eda255a4b6414f86View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-006y-9000000000-130eb5f4414426e03667View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9100000000-c096d08ca715d97cd732View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-60) , Positivesplash10-02tc-9200000000-83a0a6ad4fc1b407e570View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positivesplash10-03xu-9400000000-acd0cfd54af7d6a55283View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-03di-0900000000-309fe212c929f3c6a930View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-03di-6900000000-55a7de75a40eab61da8bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9000000000-1c3caab26eb7e359db92View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-7494d4e611a73ecb79eaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-ed4046b040337db620d8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-03di-0900000000-ff54f3083ce4ccccfd95View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-03di-0900000000-6728c1eb6f68b40c09f8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-1900000000-0029cbdcaa1377a4d03eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0229-9400000000-c227e1deb392170cb323View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9000000000-3cf6f9fc3ab6890266acView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-4900000000-67a3d94ab649e28bda13View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9100000000-bbf50de54fc413b6588eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-98042b91f1087b0c2563View in MoNA
MSMass Spectrum (Electron Ionization)splash10-03xu-9400000000-d7ffe72f606f1af3349bView in MoNA
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,1H] 2D NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Allgayer H, Kolb M, Stuber V, Kruis W: Effects of bile acids on base hydroxylation in a model of human colonic mucosal DNA. Cancer Detect Prev. 2002;26(1):85-9. Pubmed: 12088208
  • Ban, J., Vitale, L., Kos, E. (1972). "Thymine and uracil catabolism in Escherichia coli." J Gen Microbiol 73:267-272. Pubmed: 4567228
  • Bayer AS, Galpin JE, Theofilopoulos AN, Guze LB: Neurological disease associated with Mycoplasma pneumoniae pneumonitis: demonstration of viable Mycoplasma pneumoniae in cerebrospinal fluid and blood by radioisotopic and immunofluorescent tissue culture techniques. Ann Intern Med. 1981 Jan;94(1):15-20. Pubmed: 6778283
  • DeAngelis LM, Kreis W, Chan K, Dantis E, Akerman S: Pharmacokinetics of ara-C and ara-U in plasma and CSF after high-dose administration of cytosine arabinoside. Cancer Chemother Pharmacol. 1992;29(3):173-7. Pubmed: 1733548
  • Duthie SJ, Hawdon A: DNA instability (strand breakage, uracil misincorporation, and defective repair) is increased by folic acid depletion in human lymphocytes in vitro. FASEB J. 1998 Nov;12(14):1491-7. Pubmed: 9806758
  • Duthie SJ, McMillan P: Uracil misincorporation in human DNA detected using single cell gel electrophoresis. Carcinogenesis. 1997 Sep;18(9):1709-14. Pubmed: 9328165
  • Feliu J, Mel R, Borrega P, Lopez Gomez L, Escudero P, Dorta J, Castro J, Vazquez-Estevez SE, Bolanos M, Espinosa E, Gonzalez Baron M: Phase II study of a fixed dose-rate infusion of gemcitabine associated with uracil/tegafur in advanced carcinoma of the pancreas. Ann Oncol. 2002 Nov;13(11):1756-62. Pubmed: 12419748
  • Hanaue H, Kurosawa T, Kitano Y, Miyakawa S, Nemoto A, Yamamoto H, Asagoe T, Takada T, Yasuda H, Shikata J: Anticancer drug distribution in lymph and blood during adjuvant chemotherapy after surgery for gastric carcinoma. A study with a combined preparation of 1-(2-tetrahydrofuryl)-5-fluorouracil and uracil. Cancer. 1987 May 1;59(9):1571-6. Pubmed: 3103905
  • Hofmann U, Schwab M, Seefried S, Marx C, Zanger UM, Eichelbaum M, Murdter TE: Sensitive method for the quantification of urinary pyrimidine metabolites in healthy adults by gas chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 5;791(1-2):371-80. Pubmed: 12798197
  • Jakobs C, Sweetman L, Nyhan WL, Gruenke L, Craig JC, Wadman SK: Stable isotope dilution analysis of orotic acid and uracil in amniotic fluid. Clin Chim Acta. 1984 Nov 15;143(2):123-33. Pubmed: 6391739
  • Jiang H, Jiang J, Hu P, Hu Y: Measurement of endogenous uracil and dihydrouracil in plasma and urine of normal subjects by liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Mar 25;769(1):169-76. Pubmed: 11936689
  • 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
  • Mani S, Kugler JW, Sciortino DF, Garcia JC, Ansari RH, Humerickhouse R, Michelassi F, Posner MC, Shulman KL, Schilsky RL, List M, Vokes EE, Benner S: Phase II trial of uracil/tegafur (UFT) plus leucovorin in patients with advanced pancreatic carcinoma: a University of Chicago phase II consortium study. Ann Oncol. 1998 Sep;9(9):1035-7. Pubmed: 9818081
  • Mashiyama ST, Courtemanche C, Elson-Schwab I, Crott J, Lee BL, Ong CN, Fenech M, Ames BN: Uracil in DNA, determined by an improved assay, is increased when deoxynucleosides are added to folate-deficient cultured human lymphocytes. Anal Biochem. 2004 Jul 1;330(1):58-69. Pubmed: 15183762
  • Spector T, Harrington JA, Porter DJ: 5-Ethynyluracil (776C85): inactivation of dihydropyrimidine dehydrogenase in vivo. Biochem Pharmacol. 1993 Dec 14;46(12):2243-8. Pubmed: 8274158
  • 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
  • Stover PJ, Garza C: Bringing individuality to public health recommendations. J Nutr. 2002 Aug;132(8 Suppl):2476S-2480S. Pubmed: 12163715
  • Sweatman BC, Farrant RD, Holmes E, Ghauri FY, Nicholson JK, Lindon JC: 600 MHz 1H-NMR spectroscopy of human cerebrospinal fluid: effects of sample manipulation and assignment of resonances. J Pharm Biomed Anal. 1993 Aug;11(8):651-64. Pubmed: 8257730
  • Tomita T, Tajima T, Ishibashi M, Tagaya N, Aoki H, Itoh S, Kadowaki A, Kogure H, Tajima Y: [Study on the concentrations of 5-fluorouracil (5-FU), tegafur (ET) and uracil in bile: comparison of UFT or FT] Gan To Kagaku Ryoho. 1989 Dec;16(12):3755-62. Pubmed: 2512859
  • 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
  • van Kuilenburg AB, van Lenthe H, Loffler M, van Gennip AH: Analysis of pyrimidine synthesis "de novo" intermediates in urine and dried urine filter- paper strips with HPLC-electrospray tandem mass spectrometry. Clin Chem. 2004 Nov;50(11):2117-24. Epub 2004 Sep 16. Pubmed: 15375016
  • van Lenthe H, van Kuilenburg AB, Ito T, Bootsma AH, van Cruchten A, Wada Y, van Gennip AH: Defects in pyrimidine degradation identified by HPLC-electrospray tandem mass spectrometry of urine specimens or urine-soaked filter paper strips. Clin Chem. 2000 Dec;46(12):1916-22. Pubmed: 11106323
  • Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659
  • 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: Burckhalter, J. H.; Scarborough, Homer C. The synthesis of uracils as anticonvulsants. Journal of the American Pharmaceutical Association (1912-1977) (1955), 44 545-50.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID17568
HMDB IDHMDB00300
Pubchem Compound ID1174
Kegg IDC00106
ChemSpider ID1141
WikipediaUracil
BioCyc IDURACIL
EcoCyc IDURACIL
Ligand ExpoURA

Enzymes

Protein Details
• Uracil phosphoribosyltransferase
General function:
Involved in nucleoside metabolic process
Specific function:
Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
Gene Name:
upp
Locus Tag:
PA4646
Molecular weight:
22.9 kDa
Reactions
UMP + diphosphate = uracil + 5-phospho-alpha-D-ribose 1-diphosphate.
Protein Details
• Cytosine deaminase
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Specific function:
Cytosine + H(2)O = uracil + NH(3)
Gene Name:
codA
Locus Tag:
PA0437
Molecular weight:
47.1 kDa
Reactions
Cytosine + H(2)O = uracil + NH(3).

Transporters

Protein Details
• Uracil permease
General function:
Involved in transporter activity
Specific function:
Transport of uracil in the cell
Gene Name:
uraA
Locus Tag:
PA4647
Molecular weight:
44.2 kDa