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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 08:02:49 UTC
Update Date2021-09-24 08:02:50 UTC
HMDB IDHMDB0304210
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,6-dihydrothymine
DescriptionDihydrothymine, 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).
Structure
Thumb
Synonyms
ValueSource
5,6-Dihydro-5-methyluracilChEBI
5-Methyl-5,6-dihydrouracilChEBI
5,6-DihydrothymineHMDB, MeSH
5-Methyl-hydrouracilHMDB
5-Methyldihydropyrimidine-2,4(1H,3H)-dioneHMDB
dihydro-5-Methyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-MethyldihydrouracilMeSH, HMDB
5,6-Dihydrothymine, (S)-isomerMeSH, HMDB
Chemical FormulaC5H8N2O2
Average Molecular Weight128.1292
Monoisotopic Molecular Weight128.05857751
IUPAC Name5-methyl-1,3-diazinane-2,4-dione
Traditional Namedihydrothymine
CAS Registry NumberNot Available
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 KeyNBAKTGXDIBVZOO-UHFFFAOYSA-N
Chemical Taxonomy
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.).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassDiazines
Sub ClassPyrimidines and pyrimidine derivatives
Direct ParentHydropyrimidines
Alternative Parents
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
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
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 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity30.32 m³·mol⁻¹ChemAxon
Polarizability12.03 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+127.10632859911
AllCCS[M+H-H2O]+122.39232859911
AllCCS[M+Na]+132.77732859911
AllCCS[M+NH4]+131.50732859911
AllCCS[M-H]-124.41232859911
AllCCS[M+Na-2H]-126.60632859911
AllCCS[M+HCOO]-129.05732859911
DeepCCS[M+H]+130.15630932474
DeepCCS[M-H]-127.20730932474
DeepCCS[M-2H]-163.50830932474
DeepCCS[M+Na]+138.74430932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5,6-dihydrothymine,1TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)NC1=O1409.1Semi standard non polar33892256
5,6-dihydrothymine,1TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)NC1=O1398.2Standard non polar33892256
5,6-dihydrothymine,1TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)NC1=O2363.5Standard polar33892256
5,6-dihydrothymine,1TMS,isomer #2CC1CNC(=O)N([Si](C)(C)C)C1=O1361.4Semi standard non polar33892256
5,6-dihydrothymine,1TMS,isomer #2CC1CNC(=O)N([Si](C)(C)C)C1=O1344.6Standard non polar33892256
5,6-dihydrothymine,1TMS,isomer #2CC1CNC(=O)N([Si](C)(C)C)C1=O2297.0Standard polar33892256
5,6-dihydrothymine,2TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1405.0Semi standard non polar33892256
5,6-dihydrothymine,2TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1470.8Standard non polar33892256
5,6-dihydrothymine,2TMS,isomer #1CC1CN([Si](C)(C)C)C(=O)N([Si](C)(C)C)C1=O1886.6Standard polar33892256
5,6-dihydrothymine,1TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O1679.0Semi standard non polar33892256
5,6-dihydrothymine,1TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O1653.3Standard non polar33892256
5,6-dihydrothymine,1TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)NC1=O2567.4Standard polar33892256
5,6-dihydrothymine,1TBDMS,isomer #2CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O1628.5Semi standard non polar33892256
5,6-dihydrothymine,1TBDMS,isomer #2CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O1594.2Standard non polar33892256
5,6-dihydrothymine,1TBDMS,isomer #2CC1CNC(=O)N([Si](C)(C)C(C)(C)C)C1=O2365.6Standard polar33892256
5,6-dihydrothymine,2TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O1850.7Semi standard non polar33892256
5,6-dihydrothymine,2TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O1943.9Standard non polar33892256
5,6-dihydrothymine,2TBDMS,isomer #1CC1CN([Si](C)(C)C(C)(C)C)C(=O)N([Si](C)(C)C(C)(C)C)C1=O2077.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 5,6-dihydrothymine GC-MS (1 TMS)splash10-000i-5900000000-0b84b9786838d29e07ab2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 5,6-dihydrothymine GC-MS (2 TMS)splash10-0zmi-8980000000-d75d30c6e5fdb4643aa52014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized)splash10-000i-5900000000-0b84b9786838d29e07ab2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized)splash10-0zmi-8980000000-d75d30c6e5fdb4643aa52017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-dihydrothymine GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9300000000-05ab95b9effabc03847d2017-09-01Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-004l-9200000000-873ae62dcdf602237ec12014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 10V, Positive-QTOF (Annotated)splash10-004i-8900000000-db662635cbae4d48204b2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 25V, Positive-QTOF (Annotated)splash10-0006-9000000000-c3960ffe99d74c6170002012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5,6-dihydrothymine Quattro_QQQ 40V, Positive-QTOF (Annotated)splash10-0006-9000000000-9a6c2715f931ff0841572012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOFsplash10-004i-0900000000-b0b2721bf2e4a74bbba22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOFsplash10-0a4l-9100000000-b89dfebf5db699f3651c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOFsplash10-052f-9000000000-97f152f0bbe6fb600c5c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOFsplash10-004i-3900000000-98c26fdc1559c4c1afc22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOFsplash10-0006-9000000000-320f4c88705757a63b752017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOFsplash10-0006-9000000000-76fbb95e0354defdb94e2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Positive-QTOFsplash10-004i-0900000000-7c6c3743140aa087d39c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Positive-QTOFsplash10-004i-4900000000-70eb9f3b90f3b230f5932021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Positive-QTOFsplash10-0a4l-9000000000-e84dd91c5dd8c38010f72021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 10V, Negative-QTOFsplash10-004i-3900000000-b1b06bf61dca14c340152021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 20V, Negative-QTOFsplash10-0006-9200000000-a8831b6e3dbc59c569632021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-dihydrothymine 40V, Negative-QTOFsplash10-0006-9000000000-90726b17dc36e29c52992021-10-21Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Experimental 1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Experimental 2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)2012-12-04Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030555
KNApSAcK IDC00052265
Chemspider ID84456
KEGG Compound IDC00906
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27468
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available