Human Metabolome Database Version 3.5

Showing metabocard for Dihydrothymine (HMDB00079)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:07:52 -0700
HMDB ID HMDB00079
Secondary Accession Numbers None
Metabolite Identification
Common 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. Patients with dihydropyrimidinase deficiency exhibit highly increased concentrations of 5, 6-dihydrouracil and 5, 6-dihydrothymine and moderately increased concentrations of uracil and thymine can be detected in urine.
Structure Thumb
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. 5,6-Dihydro-5-methyluracil
  2. 5,6-Dihydrothymine
  3. 5-Methyl-5,6-dihydrouracil
  4. 5-Methyl-Hydrouracil
  5. 5-Methyldihydropyrimidine-2,4(1H,3H)-dione
  6. Dihydro-5-methyl-2,4(1H,3H)-Pyrimidinedione
  7. Dihydrothymine
Chemical Formula C5H8N2O2
Average Molecular Weight 128.1292
Monoisotopic Molecular Weight 128.05857751
IUPAC Name 5-methyl-1,3-diazinane-2,4-dione
Traditional IUPAC Name dihydrothymine
CAS Registry Number 696-04-8
SMILES CC1CNC(=O)NC1=O
InChI Identifier InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9)
InChI Key NBAKTGXDIBVZOO-UHFFFAOYSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Aliphatic Heteromonocyclic Compounds
Class Diazines
Sub Class Pyrimidines and Pyrimidine Derivatives
Other Descriptors
  • Aliphatic Heteromonocyclic Compounds
  • Pyrimidines and Pyrimidine Derivatives
  • Ureides
  • a base derivative(Cyc)
  • a pyrimidine-related compound(Cyc)
  • pyrimidone(ChEBI)
Substituents
  • Carboxamide Group
  • Carboxylic Acid Imide, N Unsubstituted
  • Urea
Direct Parent Pyrimidones
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction Not Available
Application Not Available
Cellular locations
  • Cytoplasm
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 18.7 g/L ALOGPS
LogP -0.80 ALOGPS
LogP -0.67 ChemAxon
LogS -0.84 ALOGPS
pKa (strongest acidic) 11.7 ChemAxon
pKa (strongest basic) -7.4 ChemAxon
Hydrogen Acceptor Count 2 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 58.2 A2 ChemAxon
Rotatable Bond Count 0 ChemAxon
Refractivity 30.32 ChemAxon
Polarizability 12.03 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum GC-MS
MS/MS Spectrum GC-MS
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Prostate
Pathways
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
1.1 +/- 0.3 uM Adult (>18 years old) Not Specified Normal
Urine Detected and Quantified
0.4 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
5.00 (0.00-10.00) umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
2.4 (1.3-4.4) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Urine Detected and Quantified
0.40 (0.17-0.64) umol/mmol creatinine Adult (>18 years old) Male Normal
Urine Detected and Quantified
0.57 (0.21-0.94) umol/mmol creatinine Adult (>18 years old) Female Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Cerebrospinal Fluid (CSF) Detected and Quantified 0.0 - 24.0 uM Not Specified Both Dihydropyrimidinase deficiency
Cerebrospinal Fluid (CSF) Detected and Quantified 4.0 - 5.2 uM Adult (>18 years old) Not Specified Beta-ureidopropionase deficiency
Associated Disorders and Diseases
Disease References
Dihydropyrimidinase deficiency
  • van Kuilenburg AB, Meijer J, Dobritzsch D, Meinsma R, Duran M, Lohkamp B, Zoetekouw L, Abeling NG, van Tinteren HL, Bosch AM: Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency. Mol Genet Metab. 2007 Jun;91(2):157-64. Epub 2007 Mar 26. Pubmed: 17383919 Link_out
      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
          Associated OMIM IDs
          • 222748 Link_out (Dihydropyrimidinase deficiency)
          • 613161 Link_out (Beta-ureidopropionase deficiency)
          DrugBank ID Not Available
          DrugBank Metabolite ID Not Available
          Phenol Explorer Compound ID Not Available
          Phenol Explorer Metabolite ID Not Available
          FoodDB ID FDB021892
          KNApSAcK ID Not Available
          Chemspider ID 84456 Link_out
          KEGG Compound ID C00906 Link_out
          BioCyc ID DIHYDRO-THYMINE Link_out
          BiGG ID 36347 Link_out
          Wikipedia Link Not Available
          NuGOwiki Link HMDB00079 Link_out
          Metagene Link HMDB00079 Link_out
          METLIN ID 5135 Link_out
          PubChem Compound 93556 Link_out
          PDB ID Not Available
          ChEBI ID 27468 Link_out
          References
          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)
          General References
          1. 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 Link_out
          2. 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
          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 Link_out
          4. 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 Link_out
          5. 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 Link_out
          6. 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 Link_out
          7. 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 Link_out
          8. 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 Link_out
          9. 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

          Enzymes
          Name: Dihydropyrimidinase
          Reactions:
          Dihydrothymine + Water unknown Ureidoisobutyric acid details
          Gene Name: DPYS
          Uniprot ID: Q14117 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Dihydropyrimidine dehydrogenase [NADP(+)]
          Reactions:
          Dihydrothymine + NADP unknown Thymine + NADPH + Hydrogen Ion details
          Gene Name: DPYD
          Uniprot ID: Q12882 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA