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-9300000000-6e24b5b6d36e07dd73d02018-05-25View Spectrum
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-0900000000-1c2ba2f2aace4a76cdea2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5d2012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a6512012-07-24View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb792012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf22012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c52012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e7062012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5f2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef4919642012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f742012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a318142012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abc2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e142012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838c2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce52012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f42012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ec2012-08-31View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb792017-09-14View Spectrum
MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf22017-09-14View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-9ad72ff6cb2e2dfab9112016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-3b1e6c50c2450e1236482016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-6900000000-d30b05dfe1b6d25ebd2b2016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052g-1940000000-ce16baa1ceb8a83565c22016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-3920000000-c6ff3f238b6fed0076352016-09-12View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-104a4f5a4fe8a0ed5ca32016-09-12View Spectrum
NMR
TypeDescriptionView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR13C NMR Spectrum (1D, D2O, experimental)Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Spectrum
2D NMR[1H, 1H]-TOCSY. Unexported temporarily by An Chi on Oct 15, 2021 until json or nmrML file is generated. 2D NMR Spectrum (experimental)Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Spectrum
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