Human Metabolome Database Version 3.5

Showing metabocard for Uracil (HMDB00300)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:16 -0700
HMDB ID HMDB00300
Secondary Accession Numbers None
Metabolite Identification
Common 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's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. UDP and UTP regulate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose in the liver and other tissues in the process of carbohydrate metabolism. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 2,4-Dihydroxypyrimidine
  2. 2,4-Dioxopyrimidine
  3. 2,4-Pyrimidinediol
  4. 2,4-Pyrimidinedione
  5. Hybar X
  6. Pirod
  7. Pyrod
  8. Uracil
Chemical Formula C4H4N2O2
Average Molecular Weight 112.0868
Monoisotopic Molecular Weight 112.027277382
IUPAC Name 1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name uracil
CAS Registry Number 66-22-8
SMILES O=C1NC=CC(=O)N1
InChI Identifier InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
InChI Key ISAKRJDGNUQOIC-UHFFFAOYSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aromatic Heteromonocyclic Compounds
Class Diazines
Sub Class Pyrimidines and Pyrimidine Derivatives
Other Descriptors
  • Pyrimidines and Pyrimidine Derivatives
  • Pyrimidines(KEGG)
  • a pyrimidine base(Cyc)
  • a pyrimidine-related compound(Cyc)
  • pyrimidine nucleobase(ChEBI)
  • pyrimidone(ChEBI)
Substituents
  • Hydropyrimidine
Direct Parent Pyrimidones
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Pantothenate and CoA biosynthesis
  • Component of Pyrimidine metabolism
  • Component of beta-Alanine metabolism
Application Not Available
Cellular locations
  • Extracellular
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 330 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 3.6 mg/mL Not Available
LogP -1.07 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 26.5 g/L ALOGPS
LogP -1.20 ALOGPS
LogP -0.86 ChemAxon
LogS -0.63 ALOGPS
pKa (strongest acidic) 9.77 ChemAxon
pKa (strongest basic) -5.5 ChemAxon
Hydrogen Acceptor Count 2 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 58.2 A2 ChemAxon
Rotatable Bond Count 0 ChemAxon
Refractivity 25.97 ChemAxon
Polarizability 9.37 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
Gas-MS Spectrum
13C NMR Spectrum
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum EI-B (HITACHI M-60)
MS/MS Spectrum EI-B (HITACHI M-80)
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies )
MS/MS Spectrum GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
MS/MS Spectrum LC-ESI-QTOF (UPLC Q-Tof Premier, Waters)
MS/MS Spectrum GC-MS
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • All Tissues
  • Prostate
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Beta-Alanine Metabolism SMP00007 map00410 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Amniotic Fluid Detected and Quantified
0.87 +/- 0.69 uM Adult (>18 years old) Female Normal
Blood Detected and Quantified
0.17 (0.097-0.26) uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
2.10 +/- 1.02 uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
0.1 +/- 0.2 uM Adult (>18 years old) Both Normal
Urine Detected but not Quantified
Not Applicable Adult (>18 years old) Male Normal
Urine Detected and Quantified
12.0 (2.0-22.0) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
2.5 (2.37-3.5) umol/mmol creatinine Adult (>18 years old) Both Normal
  • Geigy Scient...
Urine Detected and Quantified
10.13 +/- 5.43 umol/mmol creatinine Children (1-13 year old) Both Normal
Urine Detected and Quantified
6.81 +/- 5.09 umol/mmol creatinine Adolescent (13-18 years old) Both Normal
Urine Detected and Quantified
12.29 +/- 5.78 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
9.5 (2.6-22.8) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
4.99 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 2.25 +/- 0.98 uM Adult (>18 years old) Both Canavan disease
Urine Detected and Quantified 35.0 (20.0-50.0) umol/mmol creatinine Children (1-13 year old) Both Argininemia
Urine Detected and Quantified 265.0 (30.0-500.0) umol/mmol creatinine Children (1-13 year old) Both Carbamoyl phosphate synthetase deficiency
Urine Detected and Quantified 100.0 (50.0-150.0) umol/mmol creatinine Children (1-13 year old) Both Dihydropyrimidine dehydrogenase deficiency
Urine Detected and Quantified 6.00 +/- 4.00 umol/mmol creatinine Adult (>18 years old) Both Hypertension
Urine Detected and Quantified 5.00 +/- 4.00 umol/mmol creatinine Adult (>18 years old) Both Cerebral infarction
Urine Detected and Quantified 8.00 +/- 13.00 umol/mmol creatinine Adult (>18 years old) Both Malignancy
Urine Detected and Quantified 7.00 +/- 6.00 umol/mmol creatinine Adult (>18 years old) Both Liver dysfunction
Urine Detected and Quantified 20.24 +/- 7.24 umol/mmol creatinine Adult (>18 years old) Both Canavan disease
Urine Detected and Quantified 6.6 +/- 2.5 umol/mmol creatinine Adult (>18 years old) Both Nephropathy
Associated Disorders and Diseases
Disease References
Canavan disease
  • Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832 Link_out
      Argininemia
          Carbamoyl Phosphate Synthetase Deficiency
              Dihydropyrimidine dehydrogenase deficiency
                  Hypertension
                  • Hayashi K, Kidouchi K, Sumi S, Mizokami M, Orito E, Kumada K, Ueda R, Wada Y: Possible prediction of adverse reactions to pyrimidine chemotherapy from urinary pyrimidine levels and a case of asymptomatic adult dihydropyrimidinuria. Clin Cancer Res. 1996 Dec;2(12):1937-41. Pubmed: 9816152 Link_out
                      Associated OMIM IDs
                      DrugBank ID DB03419 Link_out
                      DrugBank Metabolite ID Not Available
                      Phenol Explorer Compound ID Not Available
                      Phenol Explorer Metabolite ID Not Available
                      FoodDB ID FDB006426
                      KNApSAcK ID C00001513 Link_out
                      Chemspider ID 1141 Link_out
                      KEGG Compound ID C00106 Link_out
                      BioCyc ID URACIL Link_out
                      BiGG ID 33879 Link_out
                      Wikipedia Link Uracil Link_out
                      NuGOwiki Link HMDB00300 Link_out
                      Metagene Link HMDB00300 Link_out
                      METLIN ID 258 Link_out
                      PubChem Compound 1174 Link_out
                      PDB ID URA Link_out
                      ChEBI ID 17568 Link_out
                      References
                      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)
                      General References
                      1. 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 Link_out
                      2. 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 Link_out
                      3. 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 Link_out
                      4. 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 Link_out
                      5. Duthie SJ, McMillan P: Uracil misincorporation in human DNA detected using single cell gel electrophoresis. Carcinogenesis. 1997 Sep;18(9):1709-14. Pubmed: 9328165 Link_out
                      6. 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 Link_out
                      7. 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 Link_out
                      8. 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 Link_out
                      9. 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 Link_out
                      10. 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 Link_out
                      11. 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 Link_out
                      12. Stover PJ, Garza C: Bringing individuality to public health recommendations. J Nutr. 2002 Aug;132(8 Suppl):2476S-2480S. Pubmed: 12163715 Link_out
                      13. 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 Link_out
                      14. 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 Link_out
                      15. 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 Link_out
                      16. 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 Link_out
                      17. 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 Link_out
                      18. 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 Link_out
                      19. 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 Link_out

                      Enzymes
                      Name: Dihydropyrimidine dehydrogenase [NADP(+)]
                      Reactions:
                      Dihydrouracil + NADP unknown Uracil + NADPH details
                      Dihydrouracil + NADP unknown Uracil + NADPH + Hydrogen Ion details
                      Gene Name: DPYD
                      Uniprot ID: Q12882 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Purine nucleoside phosphorylase
                      Reactions:
                      Deoxyuridine + Phosphoric acid unknown Uracil + Deoxyribose 1-phosphate details
                      Gene Name: PNP
                      Uniprot ID: P00491 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Thymidine phosphorylase
                      Reactions:
                      Deoxyuridine + Phosphoric acid unknown Uracil + Deoxyribose 1-phosphate details
                      Gene Name: TYMP
                      Uniprot ID: P19971 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Uridine phosphorylase 1
                      Reactions:
                      Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphate details
                      Gene Name: UPP1
                      Uniprot ID: Q16831 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Uridine phosphorylase 2
                      Reactions:
                      Uridine + Phosphoric acid unknown Uracil + Ribose 1-phosphate details
                      Gene Name: UPP2
                      Uniprot ID: O95045 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Uridine-cytidine kinase-like 1
                      Reactions: Not Available
                      Gene Name: UCKL1
                      Uniprot ID: Q9NWZ5 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Uracil phosphoribosyltransferase homolog
                      Reactions:
                      Uridine 5'-monophosphate + Pyrophosphate unknown Uracil + Phosphoribosyl pyrophosphate details
                      Gene Name: UPRT
                      Uniprot ID: Q96BW1 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA
                      Name: Uracil nucleotide/cysteinyl leukotriene receptor
                      Reactions: Not Available
                      Gene Name: GPR17
                      Uniprot ID: Q13304 Link_out
                      Protein Sequence: FASTA
                      Gene Sequence: FASTA