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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-10-07 20:39:31 UTC
NP-MRD IDNP0000530
Secondary Accession NumbersNone
Natural Product Identification
Common NameUracil
DescriptionUracil, also known as U, belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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. Uracil is a common naturally occurring pyrimidine found in RNA. It base pairs with adenine and is replaced by thymine in DNA. Uracil is one of the four nucleobases in RNA that are represented by the letters A, G, C and U. Methylation of uracil produces thymine. The name "uracil" was coined in 1885 by the German chemist Robert Behrend, who was attempting to synthesize derivatives of uric acid. Originally discovered in 1900, uracil was isolated by hydrolysis of yeast nuclein that was found in bovine thymus and spleen, herring sperm, and wheat germ. Uracil exists in all living species, ranging from bacteria to plants to humans. 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 an allosteric regulator and a coenzyme for many important biochemical reactions. Uracil (via the nucleoside uridine) can be phosphorylated by various kinases to produce UMP, UDP and UTP. UDP and UTP regulate carbamoyl phosphate synthetase II (CPSase II) activity in animals. Uracil is also involved in the biosynthesis of polysaccharides and in the transport of sugars containing aldehydes. Within humans, uracil participates in a number of enzymatic reactions. In particular, uracil and ribose 1-phosphate can be biosynthesized from uridine; which is mediated by the enzyme uridine phosphorylase 2. In addition, uracil can be converted into dihydrouracil through the action of the enzyme dihydropyrimidine dehydrogenase [NADP(+)]. Uracil is rarely found in DNA, and this may have been an evolutionary change to increase genetic stability. This is because cytosine can deaminate spontaneously to produce uracil through hydrolytic deamination. Therefore, if there were an organism that used uracil in its DNA, the deamination of cytosine (which undergoes base pairing with guanine) would lead to formation of uracil (which would base pair with adenine) during DNA synthesis. Uracil can be used for drug delivery and as a pharmaceutical. When elemental fluorine reacts with uracil, it produces 5-fluorouracil. 5-Fluorouracil is an anticancer drug (antimetabolite) that mimics uracil during the nucleic acid (i.E. RNA) synthesis and transcription process. Because 5-fluorouracil is similar in shape to, but does not undergo the same chemistry as, uracil, the drug inhibits RNA replication enzymes, thereby blocking RNA synthesis and stopping the growth of cancerous cells.
Structure
Thumb
Synonyms
ValueSource
2,4(1H,3H)-PyrimidinedioneChEBI
2,4-DioxopyrimidineChEBI
2,4-PyrimidinedioneChEBI
UChEBI
UraChEBI
UrazilChEBI
2,4-DihydroxypyrimidineHMDB
2,4-PyrimidinediolHMDB
Hybar XHMDB
PirodHMDB
PyrodHMDB
Chemical FormulaC4H4N2O2
Average Mass112.0868 Da
Monoisotopic Mass112.02728 Da
IUPAC Name1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Nameuracil
CAS Registry Number66-22-8
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 KeyISAKRJDGNUQOIC-UHFFFAOYSA-N
Spectra
Spectrum TypeDescriptionDepositor IDDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart Lab2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, simulated)V.dorna832021-08-01View Spectrum
Species
Species of Origin
Species NameSourceReference
Abelmoschus esculentus
Aconitum carmichaeliKNApSAcK Database
Aconitum carmichaeliiPlant
Actinidia chinensis
Agaricus bisporus
Agave
Allium ampeloprasum
Allium ascalonicum
Allium cepa
Allium cepa L.
Allium fistulosum
Allium sativum
Allium schoenoprasum
Allium tuberosum
Aloysia triphylla
Amaranthus
Amelanchier alnifolia
Anacardium occidentale
Ananas comosus
Anas platyrhynchos
Anatidae
Anethum graveolens
Angelica keiskei
Angelica sinensisKNApSAcK Database
Annona cherimola
Annona muricata
Annona reticulata
Annona squamosa
Anser anser
Anthriscus cerefolium
Apium graveolens
Apium graveolens var. dulce
Apium graveolens var. rapaceum
Apium graveolens var. secalinum
Arachis hypogaea
Arctium lappa
Armoracia rusticana
Artemisia dracunculus
Artemisia vulgaris
Artocarpus altilis
Artocarpus heterophyllus
Asparagus officinalis
Attalea speciosa
Auricularia auricula-judae
Auricularia polytricha
Avena sativa L.
Averrhoa carambola
Basella alba
Begonia nantoensisKNApSAcK Database
Benincasa hispida
Bertholletia excelsa
Beta vulgaris
Beta vulgaris ssp. cicla
Bison bison
Borago officinalis
Bos taurus
Bos taurus X Bison bison
Brassica alboglabra
Brassica juncea
Brassica napus
Brassica napus var. napus
Brassica oleracea
Brassica oleracea var. botrytis
Brassica oleracea var. capitata
Brassica oleracea var. gemmifera
Brassica oleracea var. gongylodes
Brassica oleracea var. italica
Brassica oleracea var. sabauda
Brassica oleracea var. viridis
Brassica rapa
Brassica rapa ssp. chinensis
Brassica rapa var. pekinensis
Brassica rapa var. rapa
Brassica ruvo
Brosimum alicastrum
Bubalus bubalis
Byrsonima crassifolia
Cajanus cajan
Canarium ovatum
Cannabis sativaCannabisDB
      Not Available
Cantharellus cibarius
Capparis spinosa
Capra aegagrus hircus
Capsicum annuum
Capsicum annuum L.
Capsicum annuum var. annuum
Capsicum chinense
Capsicum pubescens
Carica papaya L.
Carissa macrocarpa
Carthamus tinctorius
Carum carvi
Carya
Carya illinoinensis
Castanea
Castanea crenata
Castanea mollissima
Castanea sativa
Ceratonia siliqua
Cervidae
Cervus canadensis
Chamaemelum nobile
Chamerion angustifolium
Chenopodium album
Chenopodium quinoa
Chrysanthemum coronarium
Cicer arietinum
Cichorium endivia
Cichorium intybus
Cinnamomum
Cinnamomum aromaticum
Cinnamomum verum
Cirsium
Citrullus lanatus
Citrus ×limon (L.) Burm. f. (pro sp.)
Citrus aurantiifolia
Citrus latifolia
Citrus limon
Citrus maxima
Citrus paradisi
Citrus reticulata
Citrus X sinensis (L.) Osbeck (pro. sp.)
Cocos nucifera
Coffea arabica L.
Coffea canephora
Colocasia esculenta
Columba
Columbidae
Corchorus olitorius
Coriandrum sativum L.
Corydyceps militaris cv.-
Corydyceps sinensis-
Corylus
Corylus avellana
Crateva religiosa
Crocus sativusKNApSAcK Database
Cucumis melo
Cucumis metuliferus
Cucumis sativus L.
Cucurbita
Cucurbita maxima
Cucurbita moschata
Cuminum cymimum LKNApSAcK Database
Cuminum cyminum
Curcuma longa
Cydonia oblonga
Cymbopogon citratus
Cynara cardunculus
Cynara scolymus
Daucus carota
Daucus carota ssp. sativus
Dimocarpus longan
Dioscorea
Dioscorea pentaphylla
Diospyros
Diospyros kaki
Diospyros virginiana
Dromaius novaehollandiae
Durio zibethinus
Dysphania ambrosioides
Elaeis
Eleocharis dulcis
Elettaria cardamomum
Empetrum nigrum
Equus caballus
Eragrostis tef
Eriobotrya japonica
Eruca vesicaria subsp. Sativa
Eugenia javanica
Eugenia uniflora
Eutrema japonicum
Fagopyrum esculentum
Fagopyrum tataricum
Fagus
Feijoa sellowiana
Ficus carica
Ficus septicaKNApSAcK Database
Flammulina velutipes
Foeniculum vulgare
Fragaria x ananassa
Fritillaria cirrhosaKNApSAcK Database
Gallus gallus
Garcinia mangostana
Gaylussacia baccata
Ginkgo biloba
Glycine max
Gossypium
Grifola frondosa
Hedysarum alpinum
Helianthus annuus L.
Helianthus tuberosus
Herpetospermum caudigerum WALLKNApSAcK Database
Hibiscus sabbariffa
Hippophae rhamnoides
Hordeum vulgare
Hyssopus officinalis L.
Illicium verum
Ipomoea aquatica
Ipomoea batatas
Juglans
Juglans ailanthifolia
Juglans cinerea
Juglans nigra L.
Juglans regia
Junceella juncea-
Lablab purpureus
Lactuca sativa
Lagenaria siceraria
Lagopus muta
Lathyrus sativus
Laurus nobilis L.
Lens culinaris
Lentinus edodes
Lepidium sativum
Leporidae
Lepus timidus
Levisticum officinale
Linum usitatissimum
Litchi chinensis
Luffa aegyptiaca
Lupinus
Lupinus albus
Macadamia
Macadamia tetraphylla
Malpighia emarginata
Malus
Malus pumila
Mammea americana
Mangifera indica
Manihot esculenta
Manilkara zapota
Maranta arundinacea
Matricaria recutita
Matteuccia struthiopteris
Medicago sativa
Melanitta fusca
Meleagris gallopavo
Melissa officinalis L.
Mentha
Mentha aquatica
Mentha arvensis
Mentha spicata
Mentha x piperita
Mespilus germanica
Metroxylon sagu
Momordica charantia
Morchellaceae
Morella rubra
Moringa oleifera
Morus
Morus nigra
Musa acuminata
Musa x paradisiaca
Myrica
Myristica fragrans
Nelumbo
Nelumbo nucifera
Nephelium lappaceum
Numida meleagris
Nuphar lutea
Ocimum basilicum
Odocoileus
Oenothera biennis
Olea europaea
Opuntia
Opuntia cochenillifera
Opuntia macrorhiza
Origanum majorana
Origanum onites
Origanum vulgare
Origanum X majoricum
Oryctolagus
Oryza rufipogon
Oryza sativaFooDB
Ovis aries
Pachyrhizus erosus
Panax ginseng
Pangium edule
Panicum miliaceum
Passiflora edulis
Pastinaca sativa
Pediomelum esculentum
Perideridia oregana
Persea americana
Petasites japonicus
Petroselinum crispum
Phaseolus coccineus
Phaseolus lunatus
Phaseolus vulgaris
Phasianidae
Phasianus colchicus
Phoenix dactylifera
Photinia melanocarpa
Phyllostachys edulis
Physalis
Physalis philadelphica var. immaculata
Phytolacca americana
Pimenta dioica
Pimpinella anisum
Pinellia pedatisectaKNApSAcK Database
Pinus
Pinus edulis
Piper nigrum L.
Pistacia vera
Pisum sativum
Pleurotus ostreatus
Polygonum alpinum
Portulaca oleracea
Pouteria sapota
Prunus armeniaca
Prunus avium
Prunus avium L.
Prunus cerasus
Prunus domestica
Prunus dulcis
Prunus persica
Prunus persica var. nucipersica
Prunus persica var. persica
Prunus tomentosa
Prunus virginiana
Psidium cattleianum
Psidium guajava
Psophocarpus tetragonolobus
Punica granatum
Pyrus communis
Pyrus pyrifolia
Quercus
Raphanus sativus
Raphanus sativus var. longipinnatus
Raphanus sativus var. sativus
Rheum rhabarbarum
Ribes aureum
Ribes glandulosum
Ribes nigrum
Ribes rubrum
Ribes uva-crispa
Rosa
Rubus arcticus
Rubus chamaemorus
Rubus idaeus
Rubus occidentalis
Rubus spectabilis
Rumex
Rumex acetosa
Rumex articus
Sagittaria latifolia
Salix pulchra
Salvia elegans
Salvia hispanica
Salvia officinalis
Salvia rosmarinus
Sambucus nigra
Sambucus nigra L.
Satureja hortensis L.
Satureja montana
Scorzonera hispanica
Secale cereale
Sechium edule
Senna didymobotryaKNApSAcK Database
Sesamum indicum
Sesbania bispinosa
Sinapis alba
Sisymbrium
Solanum lycopersicum
Solanum lycopersicum var. cerasiforme
Solanum lycopersicum var. lycopersicum
Solanum melongena
Solanum quitoense
Solanum tuberosum
Sorbus aucuparia
Sorghum bicolor
Spinacia oleracea
Struthio camelus
Subergorgia suberosa-
Sus scrofa
Sus scrofa domestica
Syzygium aromaticum
Syzygium cumini
Syzygium jambos
Tamarindus indica
Taraxacum officinale
Tetragonia tetragonioides
Thelesperma
Thymus pulegioides
Thymus vulgaris
Tilia cordata
Tilia L.
Tragopogon porrifolius
Trigonella foenum-graecum
Triticum
Triticum aestivumKNApSAcK Database
Triticum durum
Triticum spelta
Triticum turanicum
Typha angustifolia
Vaccinium
Vaccinium angustifolium
Vaccinium angustifolium X Vaccinium corymbosum
Vaccinium arboreum
Vaccinium corymbosum
Vaccinium deliciosum
Vaccinium elliottii
Vaccinium macrocarpon
Vaccinium myrtilloides
Vaccinium myrtillus
Vaccinium ovalifolium
Vaccinium ovatum
Vaccinium oxycoccos
Vaccinium parvifolium
Vaccinium reticulatum
Vaccinium stamineum
Vaccinium uliginosum
Vaccinium vitis-idaea
Valerianella locusta
Vanilla
Verbena officinalis
Viburnum edule
Vicia faba
Vigna aconitifolia
Vigna angularis
Vigna mungo
Vigna radiata
Vigna umbellata
Vigna unguiculata
Vigna unguiculata ssp. cylindrica
Vigna unguiculata ssp. unguiculata
Vigna unguiculata var. sesquipedalis
Viscum coloratumKNApSAcK Database
Vitis
Vitis aestivalis
Vitis labrusca
Vitis rotundifolia
Vitis vinifera L.
Xanthosoma sagittifolium
Zea mays L.KNApSAcK Database
Zingiber officinale
Zizania
Zizania aquatica
Ziziphus zizyphus
Species Where Detected
Species NameSourceReference
Escherichia coliKNApSAcK Database
Homo sapiens (Urine)KNApSAcK Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrimidones. Pyrimidones 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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentPyrimidones
Alternative Parents
Substituents
  • Pyrimidone
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Urea
  • Lactam
  • Azacycle
  • 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
Experimental Properties
PropertyValueReference
Melting Point330 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.6 mg/mLNot Available
LogP-1.07Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility26.5 g/LALOGPS
logP-1.2ALOGPS
logP-0.86ChemAxon
logS-0.63ALOGPS
pKa (Strongest Acidic)8.8ChemAxon
pKa (Strongest Basic)-5.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25.97 m³·mol⁻¹ChemAxon
Polarizability9.37 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000300
DrugBank IDDB03419
Phenol Explorer Compound IDNot Available
FoodDB IDFDB006426
KNApSAcK IDC00001513
Chemspider ID1141
KEGG Compound IDC00106
BioCyc IDURACIL
BiGG ID33879
Wikipedia LinkUracil
METLIN ID258
PubChem Compound1174
PDB IDNot Available
ChEBI ID17568
Good Scents IDrw1888901
References
General References
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  2. 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. doi: 10.1038/nature07762. [PubMed:19212411 ]
  3. 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 ]
  4. 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 ]
  5. 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 ]
  6. 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 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. 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 ]
  11. 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 ]
  12. Duthie SJ, McMillan P: Uracil misincorporation in human DNA detected using single cell gel electrophoresis. Carcinogenesis. 1997 Sep;18(9):1709-14. [PubMed:9328165 ]
  13. 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 ]
  14. 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 ]
  15. 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 ]
  16. 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 ]
  17. Stover PJ, Garza C: Bringing individuality to public health recommendations. J Nutr. 2002 Aug;132(8 Suppl):2476S-2480S. [PubMed:12163715 ]
  18. 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 ]
  19. 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 ]