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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2014-06-13 18:36:49 UTC
HMDB IDHMDB00262
Secondary Accession NumbersNone
Metabolite Identification
Common NameThymine
DescriptionOne of the pyrimidine bases of living matter. Derivation: Hydrolysis of deoxyribonucleic acid, from methylcyanoacetylurea by catalytic reduction. Use: Biochemical research. (Hawley's Condensed Chemical Dictionary). Thymine is a pyrimidine nucleobase. As the name implies, thymine may be derived by methylation of uracil at the 5th carbon. Thymine is found in the nucleic acid DNA. In RNA thymine is replaced with uracil in most cases. In DNA, thymine binds to adenine via two hydrogen bonds to assist in stabilizing the nucleic acid structures.
Structure
Thumb
Synonyms
  1. 2,4-Dihydroxy-5-methylpyrimidine
  2. 4-Hydroxy-5-methylpyrimidin-2(1H)-one
  3. 5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
  4. 5-Methyl-2,4(1H,3H)-pyrimidinedione
  5. 5-Methyl-2,4-dihydroxypyrimidine
  6. 5-Methylpyrimidine-2,4-dione
  7. 5-Methyluracil
  8. Thymine
Chemical FormulaC5H6N2O2
Average Molecular Weight126.1133
Monoisotopic Molecular Weight126.042927446
IUPAC Name5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Namethymine
CAS Registry Number65-71-4
SMILES
CC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChI KeyRWQNBRDOKXIBIV-UHFFFAOYSA-N
Chemical Taxonomy
KingdomOrganic Compounds
Super ClassAromatic Heteromonocyclic Compounds
ClassDiazines
Sub ClassPyrimidines 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 ParentPyrimidones
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
ApplicationNot Available
Cellular locations
  • Extracellular
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point320 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.82 mg/mLYALKOWSKY,SH & DANNENFELSER,RM (1992)
LogP-0.62HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
water solubility10.8 g/LALOGPS
logP-0.99ALOGPS
logP-0.46ChemAxon
logS-1.1ALOGPS
pKa (strongest acidic)10.02ChemAxon
pKa (strongest basic)-5ChemAxon
physiological charge0ChemAxon
hydrogen acceptor count2ChemAxon
hydrogen donor count2ChemAxon
polar surface area58.2ChemAxon
rotatable bond count0ChemAxon
refractivity30.33ChemAxon
polarizability11.42ChemAxon
Spectra
SpectraGC-MSMS/MSLC-MS1D NMR2D NMR
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Fibroblasts
  • Prostate
  • Skin
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot Available
Normal
  • Not Applicable
details
Cerebrospinal Fluid (CSF)Detected and Quantified<5.0 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.0 - 0.1 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.10 (0.045-0.16) umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified0.16 (0.065-0.26) umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified1.0 (0.00-2.0) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified0.202 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified1390.0 +/- 150.0 uMAdult (>18 years old)Both
Solid tumors
details
Cerebrospinal Fluid (CSF)Detected and Quantified0.04 - 0.2 uMAdult (>18 years old)Not SpecifiedBeta-ureidopropionase deficiency details
UrineDetected and Quantified50.0 (20.0-80.0) umol/mmol creatinineChildren (1-13 years old)BothDihydropyrimidine dehydrogenase (DPD) deficiency details
Associated Disorders and Diseases
Disease References
Beta-ureidopropionase deficiency
  1. van Kuilenburg AB, Meinsma R, Beke E, Assmann B, Ribes A, Lorente I, Busch R, Mayatepek E, Abeling NG, van Cruchten A, Stroomer AE, van Lenthe H, Zoetekouw L, Kulik W, Hoffmann GF, Voit T, Wevers RA, Rutsch F, van Gennip AH: beta-Ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities. Hum Mol Genet. 2004 Nov 15;13(22):2793-801. Epub 2004 Sep 22. Pubmed: 15385443
Dihydropyrimidine dehydrogenase deficiency
  1. MetaGene
Thymidine treatment
  1. Leyva A, Schornagel JH, Kraal I, Wadman SK, Pinedo HM: Clinical and biochemical studies of high-dose thymidine treatment in patients with solid tumors. J Cancer Res Clin Oncol. 1984;107(3):211-6. Pubmed: 6736109
Associated OMIM IDs
  • 613161 (Beta-ureidopropionase deficiency)
  • 274270 (Dihydropyrimidine dehydrogenase deficiency)
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB021922
KNApSAcK IDNot Available
Chemspider ID1103
KEGG Compound IDC00178
BioCyc IDTHYMINE
BiGG ID34151
Wikipedia LinkThymine
NuGOwiki LinkHMDB00262
Metagene LinkHMDB00262
METLIN ID290
PubChem Compound1135
PDB IDTDR
ChEBI ID17821
References
Synthesis ReferenceZhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping. Synthesis of thymine. Zhongguo Yiyao Gongye Zazhi (1999), 30(7), 325.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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
  2. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7. Pubmed: 6656991
  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. 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
  6. Goukassian D, Gad F, Yaar M, Eller MS, Nehal US, Gilchrest BA: Mechanisms and implications of the age-associated decrease in DNA repair capacity. FASEB J. 2000 Jul;14(10):1325-34. Pubmed: 10877825
  7. Wassberg C, Backvall H, Diffey B, Ponten F, Berne B: Enhanced epidermal ultraviolet responses in chronically sun-exposed skin are dependent on previous sun exposure. Acta Derm Venereol. 2003;83(4):254-61. Pubmed: 12926795
  8. Schilsky RL, O'Laughlin K, Ratain MJ: Phase I clinical and pharmacological study of thymidine (NSC 21548) and cis-diamminedichloroplatinum(II) in patients with advanced cancer. Cancer Res. 1986 Aug;46(8):4184-8. Pubmed: 3731086
  9. Maskell R, Okubadejo OA, Payne RH, Pead L: Human infections with thymine-requiring bacteria. J Med Microbiol. 1978 Feb;11(1):33-45. Pubmed: 621731
  10. Ling G, Chadwick CA, Berne B, Potten CS, Ponten J, Ponten F: Epidermal p53 response and repair of thymine dimers in human skin after a single dose of ultraviolet radiation: effects of photoprotection. Acta Derm Venereol. 2001 May;81(2):81-6. Pubmed: 11501666
  11. Young AR, Sheehan JM, Chadwick CA, Potten CS: Protection by ultraviolet A and B sunscreens against in situ dipyrimidine photolesions in human epidermis is comparable to protection against sunburn. J Invest Dermatol. 2000 Jul;115(1):37-41. Pubmed: 10886505
  12. Maskell R, Okubadejo OA, Payne RH: Thymine-requiring bacteria associated with co-trimoxazole therapy. Lancet. 1976 Apr 17;1(7964):834-5. Pubmed: 56651
  13. Courdavault S, Baudouin C, Sauvaigo S, Mouret S, Candeias S, Charveron M, Favier A, Cadet J, Douki T: Unrepaired cyclobutane pyrimidine dimers do not prevent proliferation of UV-B-irradiated cultured human fibroblasts. Photochem Photobiol. 2004 Feb;79(2):145-51. Pubmed: 15068027
  14. Alsarra IA, Alarifi MN: Validated liquid chromatographic determination of 5-fluorouracil in human plasma. J Chromatogr B Analyt Technol Biomed Life Sci. 2004 May 25;804(2):435-9. Pubmed: 15081940
  15. Castro-Gago M, Camina F, Lojo S, Rodriguez-Segade S, Rodriguez-Nunez A: Concentrations of purine nucleotides and purine and pyrimidine bases in cerebrospinal fluid of neurologically healthy children. Eur J Clin Chem Clin Biochem. 1992 Nov;30(11):761-5. Pubmed: 1489848
  16. Placzek M, Gaube S, Kerkmann U, Gilbertz KP, Herzinger T, Haen E, Przybilla B: Ultraviolet B-induced DNA damage in human epidermis is modified by the antioxidants ascorbic acid and D-alpha-tocopherol. J Invest Dermatol. 2005 Feb;124(2):304-7. Pubmed: 15675947
  17. Thienpont LM, Van Landuyt KG, Stockl D, Saeyens W, De Keukeleire D, De Leenheer AP: Evaluation of 2-iminoimidazolidin-4-one and thymine as respective internal standards for normal-phase and reversed-phase high-performance liquid chromatographic determination of creatinine in human serum. J Chromatogr B Biomed Appl. 1995 Mar 10;665(1):63-9. Pubmed: 7795802
  18. Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25. Pubmed: 16442598
  19. Antille C, Tran C, Sorg O, Carraux P, Didierjean L, Saurat JH: Vitamin A exerts a photoprotective action in skin by absorbing ultraviolet B radiation. J Invest Dermatol. 2003 Nov;121(5):1163-7. Pubmed: 14708621

Enzymes

General function:
Involved in electron carrier activity
Specific function:
Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
Gene Name:
DPYD
Uniprot ID:
Q12882
Molecular weight:
111400.32
Reactions
Dihydrothymine + NADP → Thymine + NADPH + Hydrogen Iondetails
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
Thymidine + Phosphoric acid → Thymine + Deoxyribose 1-phosphatedetails