Record Information
Version2.0
Creation Date2012-05-31 09:56:50 -0600
Update Date2015-09-13 12:56:06 -0600
Secondary Accession Numbers
  • ECMDB00079
Identification
Name:Dihydrothymine
Description:Dihydrothymine is an intermediate breakdown product of thymine. Dihydropyrimidine dehydrogenase catalyzes the reduction of thymine to 5, 6-dihydrothymine then dihydropyrimidinase hydrolyzes 5, 6-dihydrothymine to N-carbamyl-b-alanine. Finally, beta-ureidopropionase catalyzes the conversion of N-carbamyl-b-alanine to beta-alanine.
Structure
Thumb
Synonyms:
  • 5,6-Dihydro-5-methyluracil
  • 5,6-Dihydrothymine
  • 5-Methyl-5,6-dihydrouracil
  • 5-Methyl-Hydrouracil
  • 5-Methyldihydropyrimidine-2,4(1H,3H)-dione
  • Dihydro-5-methyl-2,4(1H,3H)-Pyrimidinedione
  • Dihydrothymine
Chemical Formula:C5H8N2O2
Weight:Average: 128.1292
Monoisotopic: 128.05857751
InChI Key:NBAKTGXDIBVZOO-UHFFFAOYSA-N
InChI:InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)
CAS number:696-04-8
IUPAC Name:5-methyl-1,3-diazinane-2,4-dione
Traditional IUPAC Name:dihydrothymine
SMILES:CC1CNC(=O)NC1=O
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as ureides. These are compounds containing an ureide group with the general structure R1-CO-NH-CO-N(R)2R3, formally derived by the acylation of urea. They can be subdivided in N-acyl or N,N'-diacyl ureas.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic acids and derivatives
Sub ClassOrganic carbonic acids and derivatives
Direct ParentUreides
Alternative Parents
Substituents
  • Ureide
  • 5,6-dihydropyrimidine
  • Hydropyrimidine
  • Azacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility18.7 mg/mLALOGPS
logP-0.8ALOGPS
logP-0.67ChemAxon
logS-0.84ALOGPS
pKa (Strongest Acidic)11.7ChemAxon
pKa (Strongest Basic)-7.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area58.2 Å2ChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.32 m3·mol-1ChemAxon
Polarizability12.03 Å3ChemAxon
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 Pw000828Pw000828 greyscalePw000828 simple
Pyrimidine metabolismPW000942 Pw000942Pw000942 greyscalePw000942 simple
beta-Alanine metabolismPW000896 Pw000896Pw000896 greyscalePw000896 simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (1 TMS)splash10-000i-5900000000-0b84b9786838d29e07abView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
GC-MSGC-MS Spectrum - GC-MSsplash10-000i-5900000000-0b84b9786838d29e07abView in MoNA
GC-MSGC-MS Spectrum - GC-MSsplash10-0zmi-8980000000-d75d30c6e5fdb4643aa5View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-8900000000-db662635cbae4d48204bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-0006-9000000000-c3960ffe99d74c617000View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0006-9000000000-9a6c2715f931ff084157View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
MSMass Spectrum (Electron Ionization)splash10-004l-9200000000-873ae62dcdf602237ec1View in MoNA
1D NMR1H NMR SpectrumNot Available
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Assmann B, Hoffmann GF, Wagner L, Brautigam C, Seyberth HW, Duran M, Van Kuilenburg AB, Wevers R, Van Gennip AH: Dihydropyrimidinase deficiency and congenital microvillous atrophy: coincidence or genetic relation? J Inherit Metab Dis. 1997 Sep;20(5):681-8. Pubmed: 9323563
  • 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
  • Kobayashi K, Sumi S, Kidouchi K, Mizuno I, Mohri N, Fukui T, Akamo Y, Takeyama H, Manabe T: [A case of gastric cancer with decreased dihydropyrimidine dehydrogenase activity] Gan To Kagaku Ryoho. 1998 Jul;25(8):1217-9. Pubmed: 9679586
  • Rosenbaum K, Jahnke K, Curti B, Hagen WR, Schnackerz KD, Vanoni MA: Porcine recombinant dihydropyrimidine dehydrogenase: comparison of the spectroscopic and catalytic properties of the wild-type and C671A mutant enzymes. Biochemistry. 1998 Dec 15;37(50):17598-609. Pubmed: 9860876
  • 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
  • Sumi S, Imaeda M, Kidouchi K, Ohba S, Hamajima N, Kodama K, Togari H, Wada Y: Population and family studies of dihydropyrimidinuria: prevalence, inheritance mode, and risk of fluorouracil toxicity. Am J Med Genet. 1998 Jul 24;78(4):336-40. Pubmed: 9714435
  • Sumi S, Kidouchi K, Kondou M, Hayashi K, Dobashi K, Kouwaki M, Togari H, Wada Y: Possible prediction of adverse reactions to fluorouracil by the measurement of urinary dihydrothymine and thymine. Int J Mol Med. 1998 Oct;2(4):477-482. Pubmed: 9857238
  • Van Kuilenburg AB, Van Lenthe H, Van Gennip AH: Identification and tissue-specific expression of a NADH-dependent activity of dihydropyrimidine dehydrogenase in man. Anticancer Res. 1996 Jan-Feb;16(1):389-94. Pubmed: 8615641
  • 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
Synthesis Reference:Yamane, Tetsuo; Wyluda, Benjamin J.; Shulman, Robert G. Dihydrothymine from ultraviolet-irradiated DNA. Proceedings of the National Academy of Sciences of the United States of America (1967), 58(2), 439-42.
Material Safety Data Sheet (MSDS)Download (PDF)
External Links:
ResourceLink
CHEBI ID27468
HMDB IDHMDB00079
Pubchem Compound ID93556
Kegg IDC00906
ChemSpider ID84456
Wikipedia IDDihydrothymine
BioCyc IDDIHYDRO-THYMINE
EcoCyc IDDIHYDRO-THYMINE

Enzymes

General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
Specific function:
Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin derivatives with an aromatic side chains at the 5'-position. Has no activity on dihydropyrimidines. The physiological function is unknown
Gene Name:
hyuA
Uniprot ID:
Q46806
Molecular weight:
51025
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
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.