Record Information
Version1.0
Creation date2015-05-07 21:18:43 UTC
Update date2020-09-17 15:38:31 UTC
Primary IDFDB031201
Secondary Accession NumbersNot Available
Chemical Information
FooDB Namethymidine
DescriptionThymidine, also known as deoxythymidine or DTHD, belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2. Thymidine is an extremely weak basic (essentially neutral) compound (based on its pKa). Thymidine exists in all living species, ranging from bacteria to humans. In cell biology it is used to synchronize the cells in S phase. Within humans, thymidine participates in a number of enzymatic reactions. In particular, thymidine can be biosynthesized from 5-thymidylic acid through its interaction with the enzyme cytosolic purine 5'-nucleotidase. In addition, thymidine can be converted into 5-thymidylic acid; which is catalyzed by the enzyme thymidine kinase, cytosolic. In humans, thymidine is involved in the metabolic disorder called ump synthase deficiency (orotic aciduria). Outside of the human body, Thymidine has been detected, but not quantified in, several different foods, such as horned melons, asian pears, brassicas, japanese chestnuts, and apricots. This could make thymidine a potential biomarker for the consumption of these foods. Thymidine is a potentially toxic compound. Thymidine is non-toxic and is a naturally occurring compound that exists in all living organisms and DNA viruses. RNA does not have thymidine and has uridine instead. Thymidine is the DNA base T, which pairs with adenosine in double stranded DNA. 25% of DNA is composed of thymidine. Thymidine is a chemical compound which is a pyrimidine nucleoside. Thymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. Thymidine is a pyrimidine deoxynucleoside.
CAS Number50-89-5
Structure
Thumb
Synonyms
SynonymSource
1-(2-Deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneChEBI
2'-Deoxy-5-methyluridineChEBI
2'-DeoxythymidineChEBI
2'-ThymidineChEBI
5-Methyl-2'-deoxyuridineChEBI
DeoxythymidineChEBI
DTHDChEBI
TChEBI
Thymine 2'-deoxyribosideChEBI
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneGenerator
1-(2-Deoxy-β-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dioneGenerator
1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedioneHMDB
1-[4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dioneHMDB
2'-Deoxy-5-methyl-uridineHMDB
5-MethyldeoxyuridineHMDB
DeoxyribothymidineHMDB
DTHMDB
DThydHMDB
ThymidinHMDB
Thymine 2-desoxyribosideHMDB
Thymine deoxyribosideHMDB
Thymine-1 2-deoxy-b-D-ribofuranosideHMDB
Thymine-1 2-deoxy-beta-delta-ribofuranosideHMDB
2' DeoxythymidineHMDB
Predicted Properties
PropertyValueSource
Water Solubility66.8 g/LALOGPS
logP-1.3ALOGPS
logP-1.1ChemAxon
logS-0.56ALOGPS
pKa (Strongest Acidic)9.96ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area99.1 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.41 m³·mol⁻¹ChemAxon
Polarizability23.06 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Chemical FormulaC10H14N2O5
IUPAC name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
InChI IdentifierInChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
InChI KeyIQFYYKKMVGJFEH-XLPZGREQSA-N
Isomeric SMILESCC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
Average Molecular Weight242.2286
Monoisotopic Molecular Weight242.090271568
Classification
Description Belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. Pyrimidine 2'-deoxyribonucleosides are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 2'-deoxyribonucleosides
Alternative Parents
Substituents
  • Pyrimidine 2'-deoxyribonucleoside
  • Pyrimidone
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Pyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Route of exposure:

Source:

Biological location:

Role

Biological role:

Industrial application:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateNot Available
Physical DescriptionNot Available
Mass CompositionNot Available
Melting PointNot Available
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical RotationNot Available
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
EI-MSMass Spectrum (Electron Ionization)splash10-01dj-9300000000-6e24b5b6d36e07dd73d0Spectrum
GC-MSthymidine, 2 TMS, GC-MS Spectrumsplash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSthymidine, 3 TMS, GC-MS Spectrumsplash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSthymidine, non-derivatized, GC-MS Spectrumsplash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSthymidine, non-derivatized, GC-MS Spectrumsplash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSthymidine, non-derivatized, GC-MS Spectrumsplash10-0udi-0900000000-996530d1ea081ac2a7c7Spectrum
GC-MSthymidine, non-derivatized, GC-MS Spectrumsplash10-0l6r-0900000000-4645a52830204c8ef5d0Spectrum
GC-MSthymidine, non-derivatized, GC-MS Spectrumsplash10-0zfr-0900000000-76b8a050c10b514ed50bSpectrum
Predicted GC-MSthymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-004i-9530000000-627a60bbe3e0b90f58cbSpectrum
Predicted GC-MSthymidine, 2 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0g4i-7905000000-7b0c67709e3a5f91841aSpectrum
Predicted GC-MSthymidine, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_1_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_1_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_1_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_2_1, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_2_2, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSthymidine, TBDMS_2_3, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1c2ba2f2aace4a76cdeaSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5dSpectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a651Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c5Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e706Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5fSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef491964Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f74Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a31814Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abcSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e14Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838cSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce5Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f4Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ecSpectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-9ad72ff6cb2e2dfab911Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-3b1e6c50c2450e123648Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-6900000000-d30b05dfe1b6d25ebd2bSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052g-1940000000-ce16baa1ceb8a83565c2Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-3920000000-c6ff3f238b6fed007635Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-104a4f5a4fe8a0ed5ca3Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
1D NMR1H NMR SpectrumSpectrum
1D NMR13C NMR SpectrumSpectrum
2D NMR[1H,1H] 2D NMR SpectrumSpectrum
2D NMR[1H,13C] 2D NMR SpectrumSpectrum
ChemSpider IDNot Available
ChEMBL IDNot Available
KEGG Compound IDNot Available
Pubchem Compound IDNot Available
Pubchem Substance IDNot Available
ChEBI IDNot Available
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDNot Available
CRC / DFC (Dictionary of Food Compounds) IDNot Available
EAFUS IDNot Available
Dr. Duke IDNot Available
BIGG IDNot Available
KNApSAcK IDNot Available
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDNot Available
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / BioactivitiesNot Available
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference