Record Information |
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Version | 5.0 |
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Status | Detected but not Quantified |
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Creation Date | 2021-09-24 08:02:49 UTC |
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Update Date | 2022-09-22 18:34:37 UTC |
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HMDB ID | HMDB0304210 |
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Secondary Accession Numbers | None |
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Metabolite Identification |
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Common Name | 5,6-dihydrothymine |
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Description | Dihydrothymine, also known as 5,6-dihydro-5-methyluracil or 5,6-dihydrothymine, (S)-isomer, is a member of the class of compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.). Dihydrothymine is soluble (in water) and a very weakly acidic compound (based on its pKa). Dihydrothymine can be found in a number of food items such as hyssop, arrowroot, nopal, and red rice, which makes dihydrothymine a potential biomarker for the consumption of these food products. Dihydrothymine can be found primarily in blood, cerebrospinal fluid (CSF), saliva, and urine, as well as in human prostate tissue. Dihydrothymine exists in all living organisms, ranging from bacteria to humans. In humans, dihydrothymine is involved in the pyrimidine metabolism. Dihydrothymine is also involved in few metabolic disorders, which include beta ureidopropionase deficiency, dihydropyrimidinase deficiency, MNGIE (mitochondrial neurogastrointestinal encephalopathy), and UMP synthase deficiency (orotic aciduria). Moreover, dihydrothymine is found to be associated with beta-ureidopropionase deficiency and dihydropyrimidinase deficiency. Dihydrothymine is a non-carcinogenic (not listed by IARC) potentially toxic compound. Dihydrothymine is an intermediate in the metabolism 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. Accumulation of dihydrothymine in the body has been shown to be toxic (T3DB). |
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Structure | InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9) |
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Synonyms | Value | Source |
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5,6-Dihydro-5-methyluracil | ChEBI | 5-Methyl-5,6-dihydrouracil | ChEBI | 5,6-Dihydrothymine | HMDB, MeSH | 5-Methyl-hydrouracil | HMDB | 5-Methyldihydropyrimidine-2,4(1H,3H)-dione | HMDB | dihydro-5-Methyl-2,4(1H,3H)-pyrimidinedione | HMDB | 5-Methyldihydrouracil | MeSH, HMDB | 5,6-Dihydrothymine, (S)-isomer | MeSH, HMDB |
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Chemical Formula | C5H8N2O2 |
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Average Molecular Weight | 128.1292 |
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Monoisotopic Molecular Weight | 128.05857751 |
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IUPAC Name | 5-methyl-1,3-diazinane-2,4-dione |
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Traditional Name | dihydrothymine |
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CAS Registry Number | Not Available |
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SMILES | CC1CNC(=O)NC1=O |
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InChI Identifier | InChI=1S/C5H8N2O2/c1-3-2-6-5(9)7-4(3)8/h3H,2H2,1H3,(H2,6,7,8,9) |
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InChI Key | NBAKTGXDIBVZOO-UHFFFAOYSA-N |
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Chemical Taxonomy |
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Description | Belongs to the class of organic compounds known as hydropyrimidines. Hydropyrimidines are compounds containing a hydrogenated pyrimidine ring (i.E. Containing less than the maximum number of double bonds.). |
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Kingdom | Organic compounds |
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Super Class | Organoheterocyclic compounds |
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Class | Diazines |
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Sub Class | Pyrimidines and pyrimidine derivatives |
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Direct Parent | Hydropyrimidines |
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Alternative Parents | |
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Substituents | - 5,6-dihydropyrimidine
- Hydropyrimidine
- Azacycle
- 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
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Molecular Framework | Aliphatic heteromonocyclic compounds |
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External Descriptors | |
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Ontology |
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Physiological effect | |
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Disposition | |
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Process | |
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Role | |
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Physical Properties |
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State | Not Available |
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Experimental Molecular Properties | Property | Value | Reference |
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Melting Point | Not Available | Not Available | Boiling Point | Not Available | Not Available | Water Solubility | Not Available | Not Available | LogP | Not Available | Not Available |
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Experimental Chromatographic Properties | Not Available |
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Predicted Molecular Properties | |
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Predicted Chromatographic Properties | Predicted Collision Cross SectionsPredicted Kovats Retention IndicesDerivatizedDerivative Name / Structure | SMILES | Kovats RI Value | Column Type | Reference |
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5,6-dihydrothymine,1TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)NC1=O | 1409.1 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,1TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)NC1=O | 1398.2 | Standard non polar | 33892256 | 5,6-dihydrothymine,1TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)NC1=O | 2363.5 | Standard polar | 33892256 | 5,6-dihydrothymine,1TMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C)C1=O | 1361.4 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,1TMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C)C1=O | 1344.6 | Standard non polar | 33892256 | 5,6-dihydrothymine,1TMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C)C1=O | 2297.0 | Standard polar | 33892256 | 5,6-dihydrothymine,2TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O | 1405.0 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,2TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O | 1470.8 | Standard non polar | 33892256 | 5,6-dihydrothymine,2TMS,isomer #1 | CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O | 1886.6 | Standard polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O | 1679.0 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O | 1653.3 | Standard non polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O | 2567.4 | Standard polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O | 1628.5 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O | 1594.2 | Standard non polar | 33892256 | 5,6-dihydrothymine,1TBDMS,isomer #2 | CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O | 2365.6 | Standard polar | 33892256 | 5,6-dihydrothymine,2TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O | 1850.7 | Semi standard non polar | 33892256 | 5,6-dihydrothymine,2TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O | 1943.9 | Standard non polar | 33892256 | 5,6-dihydrothymine,2TBDMS,isomer #1 | CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O | 2077.0 | Standard polar | 33892256 |
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| GC-MS SpectraSpectrum Type | Description | Splash Key | Deposition Date | Source | View |
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Experimental GC-MS | GC-MS Spectrum - 5,6-dihydrothymine GC-MS (1 TMS) | splash10-000i-5900000000-0b84b9786838d29e07ab | 2014-06-16 | HMDB team, MONA, MassBank | View Spectrum | Experimental GC-MS | GC-MS Spectrum - 5,6-dihydrothymine GC-MS (2 TMS) | splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5 | 2014-06-16 | HMDB team, MONA, MassBank | View Spectrum | Experimental GC-MS | GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized) | splash10-000i-5900000000-0b84b9786838d29e07ab | 2017-09-12 | HMDB team, MONA, MassBank | View Spectrum | Experimental GC-MS | GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized) | splash10-0zmi-8980000000-d75d30c6e5fdb4643aa5 | 2017-09-12 | HMDB team, MONA, MassBank | View Spectrum | Predicted GC-MS | Predicted GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized) - 70eV, Positive | splash10-004i-9300000000-05ab95b9effabc03847d | 2017-09-01 | Wishart Lab | View Spectrum | MS | Mass Spectrum (Electron Ionization) | splash10-004l-9200000000-873ae62dcdf602237ec1 | 2014-09-20 | Not Available | View Spectrum |
MS/MS SpectraSpectrum Type | Description | Splash Key | Deposition Date | Source | View |
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Experimental LC-MS/MS | LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 10V, Positive-QTOF (Annotated) | splash10-004i-8900000000-db662635cbae4d48204b | 2012-07-24 | HMDB team, MONA | View Spectrum | Experimental LC-MS/MS | LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 25V, Positive-QTOF (Annotated) | splash10-0006-9000000000-c3960ffe99d74c617000 | 2012-07-24 | HMDB team, MONA | View Spectrum | Experimental LC-MS/MS | LC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 40V, Positive-QTOF (Annotated) | splash10-0006-9000000000-9a6c2715f931ff084157 | 2012-07-24 | HMDB team, MONA | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOF | splash10-004i-0900000000-b0b2721bf2e4a74bbba2 | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOF | splash10-0a4l-9100000000-b89dfebf5db699f3651c | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOF | splash10-052f-9000000000-97f152f0bbe6fb600c5c | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOF | splash10-004i-3900000000-98c26fdc1559c4c1afc2 | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOF | splash10-0006-9000000000-320f4c88705757a63b75 | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOF | splash10-0006-9000000000-76fbb95e0354defdb94e | 2017-09-01 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOF | splash10-004i-0900000000-7c6c3743140aa087d39c | 2021-10-21 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOF | splash10-004i-4900000000-70eb9f3b90f3b230f593 | 2021-10-21 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOF | splash10-0a4l-9000000000-e84dd91c5dd8c38010f7 | 2021-10-21 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOF | splash10-004i-3900000000-b1b06bf61dca14c34015 | 2021-10-21 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOF | splash10-0006-9200000000-a8831b6e3dbc59c56963 | 2021-10-21 | Wishart Lab | View Spectrum | Predicted LC-MS/MS | Predicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOF | splash10-0006-9000000000-90726b17dc36e29c5299 | 2021-10-21 | Wishart Lab | View Spectrum |
NMR SpectraSpectrum Type | Description | Deposition Date | Source | View |
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Experimental 1D NMR | 1H NMR Spectrum (1D, 600 MHz, H2O, experimental) | 2012-12-04 | Wishart Lab | View Spectrum | Experimental 2D NMR | [1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental) | 2012-12-04 | Wishart Lab | View Spectrum |
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