Record Information
Version2.0
Creation Date2012-05-31 10:25:09 -0600
Update Date2015-09-13 12:56:07 -0600
Secondary Accession Numbers
  • ECMDB00262
Identification
Name:Thymine
DescriptionThymine is a nucleobase that is also known as 5-methyluracil. As the name suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thus stabilizing the nucleic acid structures. Thymine combined with deoxyribose creates the nucleoside deoxythymidine, when it is combined with ribose it creates the nucleoside thymidine. Thymidine can be phosphorylated with one, two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP
Structure
Thumb
Synonyms:
  • 2,4-Dihydroxy-5-methylpyrimidine
  • 4-Hydroxy-5-methylpyrimidin-2(1H)-one
  • 5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
  • 5-Methyl-2,4(1H,3H)-pyrimidinedione
  • 5-Methyl-2,4-dihydroxypyrimidine
  • 5-Methylpyrimidine-2,4-dione
  • 5-Methyluracil
  • Thymine
Chemical Formula:C5H6N2O2
Weight:Average: 126.1133
Monoisotopic: 126.042927446
InChI Key:RWQNBRDOKXIBIV-UHFFFAOYSA-N
InChI:InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
CAS number:65-71-4
IUPAC Name:5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name:thymine
SMILES:CC1=CNC(=O)NC1=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached to a pyrimidine ring. 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 ParentHydroxypyrimidines
Alternative Parents
Substituents
  • Hydroxypyrimidine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:320 °C
Experimental Properties:
PropertyValueSource
Water Solubility:3.82 mg/mL [YALKOWSKY,SH & DANNENFELSER,RM (1992)]; 8 mg/mL [HMP experimental]PhysProp
LogP:-0.62 [HANSCH,C ET AL. (1995)]PhysProp
Predicted Properties
PropertyValueSource
Water Solubility10.8 g/LALOGPS
logP-0.99ALOGPS
logP-0.46ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)9.06ChemAxon
pKa (Strongest Basic)-5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.33 m³·mol⁻¹ChemAxon
Polarizability11.42 ųChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
SMPDB Pathways:
Pantothenate and CoA biosynthesisPW000828 ThumbThumb?image type=greyscaleThumb?image type=simple
Pyrimidine metabolismPW000942 ThumbThumb?image type=greyscaleThumb?image type=simple
beta-Alanine metabolismPW000896 ThumbThumb?image type=greyscaleThumb?image type=simple
pyrimidine deoxyribonucleosides degradationPW002063 ThumbThumb?image type=greyscaleThumb?image type=simple
salvage pathways of pyrimidine deoxyribonucleotidesPW002061 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • pyrimidine deoxyribonucleosides degradation PWY0-1298
  • salvage pathways of pyrimidine deoxyribonucleotides PWY0-181
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-0bt9-0960000000-50722d1f64f22b69e207View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-0bta-0940000000-ff59d40c1a93e04954abView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (2 TMS)splash10-05fr-7940000000-a0ebb190eba32aceac56View in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0ab9-1980000000-5b95ad97f31d8176a0c6View in MoNA
GC-MSGC-MS Spectrum - EI-B (Non-derivatized)splash10-004i-9500000000-74b6d7909610070d30d0View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0bt9-0960000000-50722d1f64f22b69e207View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0bta-0940000000-ff59d40c1a93e04954abView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-05fr-7940000000-a0ebb190eba32aceac56View in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0ab9-1980000000-5b95ad97f31d8176a0c6View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0bta-0930000000-a2d3bc738d3f9e60aeb7View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9500000000-33bb743c9a1a77fe4e47View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-a3779faac812139c6333View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-0900000000-a3779faac812139c6333View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0udi-9200000000-0e7d9466530de47896d9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - EI-B (HITACHI M-80) , Positivesplash10-004i-9400000000-7ff00d5a94e12e6e1701View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-004i-9100000000-1e96fdb2525aace8b29dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0a6r-9000000000-34edf89b8a99493ed897View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0a4i-9000000000-7d381bc0d559ed8150e9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0a4i-9000000000-90f8edce6ae2b6f83347View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0a4l-9000000000-445d07aed275008cfe2dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-056r-8900000000-96370e30b48d3270abaaView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-0bwc-9600000000-b988fb9252c409b19c33View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-01q9-9100000000-8c82d68e9ec8594b1fffView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-001i-9000000000-f69c5d963b845f8b3cfbView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-0a4i-0900000000-3a9af2cf67d3f113fa7fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Positivesplash10-004i-0900000000-97549ff58b84351d860cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) 30V, Positivesplash10-01q9-7900000000-5804e303580e1273f1a2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negativesplash10-004i-0900000000-deb5e6830bc01a0c870eView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-004i-9100000000-1e96fdb2525aace8b29dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0a6r-9000000000-34edf89b8a99493ed897View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-1900000000-7f378c898bdb1944116eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-057i-9400000000-df8e4d4b901c8d1334fcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0zfr-9000000000-629132689aa512d344b2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-2900000000-878180774da717dee4aeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-005c-9400000000-2bf425b661913858b12aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-87ca2758dbf67661c671View in MoNA
MSMass Spectrum (Electron Ionization)splash10-056r-9400000000-5dd0bc0194a302d8ee95View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Maskell R, Okubadejo OA, Payne RH: Thymine-requiring bacteria associated with co-trimoxazole therapy. Lancet. 1976 Apr 17;1(7964):834-5. Pubmed: 56651
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 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
  • 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
  • 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
  • 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
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)
External Links:
ResourceLink
CHEBI ID17821
HMDB IDHMDB00262
Pubchem Compound ID1135
Kegg IDC00178
ChemSpider ID1103
WikipediaThymine
BioCyc IDTHYMINE
EcoCyc IDTHYMINE
Ligand ExpoTDR

Enzymes

General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:
deoA
Uniprot ID:
P07650
Molecular weight:
47207
Reactions
Thymidine + phosphate = thymine + 2-deoxy-alpha-D-ribose 1-phosphate.
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
Uniprot ID:
P25524
Molecular weight:
47591
Reactions
Cytosine + H(2)O = uracil + NH(3).
General function:
Involved in iron-sulfur cluster binding
Specific function:
Specific function unknown
Gene Name:
yeiA
Uniprot ID:
P25889
Molecular weight:
45069
Reactions
5,6-dihydrouracil + NAD(+) = uracil + NADH.
5,6-dihydrothymine + NAD(+) = thymine + NADH.
General function:
Involved in oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
Specific function:
Part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source
Gene Name:
rutA
Uniprot ID:
P75898
Molecular weight:
42219
Reactions
Uracil + FMNH(2) + O(2) = (Z)-3-ureidoacrylate peracid + FMN + H(2)O.
Thymine + FMNH(2) + O(2) = (Z)-2-methylureidoacrylate peracid + FMN + H(2)O.
General function:
Involved in oxidoreductase activity
Specific function:
Specific function unknown
Gene Name:
yeiT
Uniprot ID:
P76440
Molecular weight:
44329
Reactions
5,6-dihydrouracil + NAD(+) = uracil + NADH.
5,6-dihydrothymine + NAD(+) = thymine + NADH.

Transporters

General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368