Showing metabocard for Thymine (BMDB0000262)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
Record Information
Version1.0
Creation Date2016-09-30 22:27:34 UTC
Update Date2020-06-04 20:48:21 UTC
BMDB IDBMDB0000262
Secondary Accession Numbers
  • BMDB00262
Metabolite Identification
Common NameThymine
DescriptionThymine, also known as 5-methyluracil, 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. Thymine exists as a solid, possibly soluble (in water), and an extremely weak basic (essentially neutral) compound (based on its pKa) molecule. Thymine exists in all living species, ranging from bacteria to humans. Thymine is a potentially toxic compound. Thymine has been found to be associated with several diseases known as colorectal cancer, thymidine treatment, and temporomandibular joint disorder; also thymine has been linked to the inborn metabolic disorders including dihydropyrimidine dehydrogenase deficiency.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2,4-Dihydroxy-5-methylpyrimidineChEBI
5-Methyl-2,4(1H,3H)-pyrimidinedioneChEBI
5-Methylpyrimidine-2,4(1H,3H)-dioneChEBI
5-MethyluracilChEBI
TChEBI
ThyChEBI
ThyminChEBI
4-Hydroxy-5-methylpyrimidin-2(1H)-oneHMDB
5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneHMDB
5-Methyl-2,4-dihydroxypyrimidineHMDB
5-Methylpyrimidine-2,4-dioneHMDB
5 MethyluracilHMDB
Chemical FormulaC5H6N2O2
Average Molecular Weight126.1133
Monoisotopic Molecular Weight126.042927446
IUPAC Name5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymine
CAS Registry Number65-71-4
SMILES
CC1=CNC(=O)NC1=O
InChI Identifier
InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChI KeyRWQNBRDOKXIBIV-UHFFFAOYSA-N
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
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point320 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.82 mg/mLYALKOWSKY,SH & DANNENFELSER,RM (1992)
LogP-0.62HANSCH,C ET AL. (1995)
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Epidermis
  • Fibroblasts
  • Liver
  • Mammary Gland
  • Milk
  • Placenta
  • Prostate Tissue
  • Ruminal Fluid
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
EpidermisExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
FibroblastsExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
LiverDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Mammary GlandDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
MilkDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
PlacentaExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Prostate TissueExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal
  • Not Applicable
 details
Ruminal FluidDetected and Quantified188 +/- 45 uMNot SpecifiedNot Specified
Normal
    • Aidin Foroutan, C...
 details
Ruminal FluidDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Ruminal FluidDetected and Quantified26.3 uMNot SpecifiedNot Specified
Normal		 details
Ruminal FluidDetected and Quantified30.1 uMNot SpecifiedNot Specified
Normal		 details
Ruminal FluidDetected and Quantified30.2 uMNot SpecifiedNot Specified
Normal		 details
Ruminal FluidDetected and Quantified39.7 uMNot SpecifiedNot Specified
Normal		 details
Ruminal FluidDetected and Quantified27 +/- 12 uMNot SpecifiedNot Specified
Normal
    • Fozia Saleem, Sou...
 details
Ruminal FluidDetected and Quantified30 +/- 14 uMNot SpecifiedNot Specified
Normal
    • Fozia Saleem, Sou...
 details
Ruminal FluidDetected and Quantified35 +/- 30 uMNot SpecifiedNot Specified
Normal
    • Fozia Saleem, Sou...
 details
Ruminal FluidDetected and Quantified40 +/- 23 uMNot SpecifiedNot Specified
Normal
    • Fozia Saleem, Sou...
 details
Ruminal FluidDetected and Quantified40 +/- 23 uMNot SpecifiedNot Specified
Normal
    • Fozia Saleem, Sou...
 details
Ruminal FluidDetected and Quantified39.78 +/- 46.65 uMNot SpecifiedNot SpecifiedNormal
    • Fozia Saleem, Sou...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Ruminal FluidDetected and Quantified30.27 +/- 29.58 uMNot SpecifiedNot SpecifiedRumen acidosis
    • Fozia Saleem, Sou...
 details
HMDB IDHMDB0000262
DrugBank IDDB03462
Phenol Explorer Compound IDNot Available
FooDB IDFDB021922
KNApSAcK IDC00001511
Chemspider ID1103
KEGG Compound IDC00178
BioCyc IDTHYMINE
BiGG ID34151
Wikipedia LinkThymine
METLIN ID290
PubChem Compound1135
PDB IDNot Available
ChEBI ID17821
References
Synthesis ReferenceZhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping. Synthesis of thymine. Zhongguo Yiyao Gongye Zazhi (1999), 30(7), 325.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
  2. Pan L, Yu J, Mi Z, Mo L, Jin H, Yao C, Ren D, Menghe B: A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation). Molecules. 2018 Mar 22;23(4). pii: molecules23040735. doi: 10.3390/molecules23040735. [PubMed:29565828 ]

Enzymes

Enzyme Details
1. Dihydropyrimidine dehydrogenase [NADP(+)]
General function:
Amino acid transport and metabolism
Specific function:
Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.
Gene Name:
DPYD
Uniprot ID:
Q28007
Molecular weight:
111697.0
Reactions
Thymine + NADP → Dihydrothymine + NADPHdetails