Human Metabolome Database Version 3.5

Showing metabocard for Thymine (HMDB00262)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-05-13 17:03:56 -0600
Secondary Accession Numbers None
Metabolite Identification
Common Name Thymine
Description One 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
  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 Formula C5H6N2O2
Average Molecular Weight 126.1133
Monoisotopic Molecular Weight 126.042927446
IUPAC Name 5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name thymine
CAS Registry Number 65-71-4
InChI Identifier InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
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)
  • Hydropyrimidine
Direct Parent Pyrimidones
Status Detected and Quantified
  • Endogenous
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
Application Not Available
Cellular locations
  • Extracellular
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point 320 °C Not Available
Boiling Point Not Available Not Available
Water Solubility 3.82 mg/mL YALKOWSKY,SH & DANNENFELSER,RM (1992)
LogP -0.62 HANSCH,C ET AL. (1995)
Predicted Properties
Property Value Source
Water Solubility 10.8 g/L ALOGPS
LogP -0.99 ALOGPS
LogP -0.46 ChemAxon
LogS -1.07 ALOGPS
pKa (strongest acidic) 10.02 ChemAxon
pKa (strongest basic) -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 30.33 ChemAxon
Polarizability 11.42 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
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-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 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)
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Fibroblasts
  • Prostate
  • Skin
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Expected but not Quantified
Not Applicable Not Available Not Available Comment Normal
  • Not Applicable
Cerebrospinal Fluid (CSF) Detected and Quantified
<5.0 uM Adult (>18 years old) Both Normal
Cerebrospinal Fluid (CSF) Detected and Quantified
0.0 - 0.1 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.10 (0.045-0.16) umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected and Quantified
0.16 (0.065-0.26) umol/mmol creatinine Adult (>18 years old) Female Normal
Urine Detected and Quantified
1.0 (0.00-2.0) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
0.202 umol/mmol creatinine Adult (>18 years old) Both Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 1390.0 +/- 150.0 uM Adult (>18 years old) Both Thymidine treatment
Cerebrospinal Fluid (CSF) Detected and Quantified 0.04 - 0.2 uM Adult (>18 years old) Not Specified Beta-ureidopropionase deficiency
Urine Detected and Quantified 50.0 (20.0-80.0) umol/mmol creatinine Children (1-13 year old) Both Dihydropyrimidine dehydrogenase deficiency
Associated Disorders and Diseases
Disease References
Beta-ureidopropionase deficiency
  • 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 Link_out
      Thymidine treatment
      • 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 Link_out
          Dihydropyrimidine dehydrogenase deficiency
              Associated OMIM IDs
              • 613161 Link_out (Beta-ureidopropionase deficiency)
              • 274270 Link_out (Dihydropyrimidine dehydrogenase deficiency)
              DrugBank ID Not Available
              DrugBank Metabolite ID Not Available
              Phenol Explorer Compound ID Not Available
              Phenol Explorer Metabolite ID Not Available
              FoodDB ID FDB021922
              KNApSAcK ID Not Available
              Chemspider ID 1103 Link_out
              KEGG Compound ID C00178 Link_out
              BioCyc ID THYMINE Link_out
              BiGG ID 34151 Link_out
              Wikipedia Link Thymine Link_out
              NuGOwiki Link HMDB00262 Link_out
              Metagene Link HMDB00262 Link_out
              METLIN ID 290 Link_out
              PubChem Compound 1135 Link_out
              PDB ID TDR Link_out
              ChEBI ID 17821 Link_out
              Synthesis Reference Zhang, 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. 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 Link_out
              2. 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 Link_out
              3. 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 Link_out
              4. 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 Link_out
              5. 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
              6. 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 Link_out
              7. 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 Link_out
              8. Maskell R, Okubadejo OA, Payne RH: Thymine-requiring bacteria associated with co-trimoxazole therapy. Lancet. 1976 Apr 17;1(7964):834-5. Pubmed: 56651 Link_out
              9. 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 Link_out
              10. 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 Link_out
              11. 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
              12. 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 Link_out
              13. 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 Link_out
              14. 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 Link_out
              15. 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 Link_out
              16. 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
              17. 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 Link_out
              18. 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 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

              Name: Dihydropyrimidine dehydrogenase [NADP(+)]
              Dihydrothymine + NADP unknown Thymine + NADPH + Hydrogen Ion details
              Gene Name: DPYD
              Uniprot ID: Q12882 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA
              Name: Thymidine phosphorylase
              Thymidine + Phosphoric acid unknown Thymine + Deoxyribose 1-phosphate details
              Gene Name: TYMP
              Uniprot ID: P19971 Link_out
              Protein Sequence: FASTA
              Gene Sequence: FASTA