Thymidine (CHEM003392)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesTargets (2)XML
Record Information
Version1.0
Creation Date2014-08-29 06:51:15 UTC
Update Date2026-05-14 18:08:35 UTC
Accession NumberCHEM003392
Identification
Common NameThymidine
ClassSmall Molecule
DescriptionThymidine is non-toxic and is a naturally occurring compound that exists in all living organisms and DNA viruses. 25% of DNA is composed of thymidine. RNA does not have thymidine and has uridine instead. Thymidine is a chemical compound which is a pyrimidine nucleoside. Thymidine is the DNA base T, which pairs with adenosine in double stranded DNA.
Contaminant Sources
  • FooDB Chemicals
  • HMDB Contaminants - Urine
  • STOFF IDENT Compounds
  • T3DB toxins
  • ToxCast & Tox21 Chemicals
Contaminant Type
  • Amine
  • Animal Toxin
  • Ether
  • Food Toxin
  • Human Neurotoxin
  • Metabolite
  • Natural Compound
  • Organic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
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
Chemical FormulaC10H14N2O5
Average Molecular Mass242.229 g/mol
Monoisotopic Mass242.090 g/mol
CAS Registry Number50-89-5
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymidine
SMILESCC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
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
Chemical Taxonomy
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
Biological Properties
StatusDetected and Not Quantified
OriginEndogenous
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Lysosome
  • Mitochondria
Biofluid LocationsNot Available
Tissue Locations
  • Adipose Tissue
  • Adrenal Gland
  • Bladder
  • Fetus
  • Fibroblasts
  • Intestine
  • Kidney
  • Muscle
  • Neuron
  • Pancreas
  • Placenta
  • Platelet
  • Prostate
  • Skeletal Muscle
  • Skin
  • Spleen
  • Stratum Corneum
  • Testes
  • Thyroid Gland
Pathways
NameSMPDB LinkKEGG Link
Pyrimidine MetabolismSMP00046 map00240
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy)SMP00202 Not Available
ApplicationsNot Available
Biological Roles
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting Point185°C (365°F)
Boiling PointNot Available
Solubility73.5 mg/mL
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0udi-1900000000-8e769118bc877facb05fSpectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0ue9-2910000000-823bcee487948a9c786fSpectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0900000000-996530d1ea081ac2a7c7Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0l6r-0900000000-4645a52830204c8ef5d0Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0zfr-0900000000-76b8a050c10b514ed50bSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-9530000000-627a60bbe3e0b90f58cbSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0g4i-7905000000-7b0c67709e3a5f91841aSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1c2ba2f2aace4a76cdeaSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-3900000000-d177672ef3f383adbb5dSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-01p9-9000000000-4483af567feecb34a651Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Negativesplash10-0006-9100000000-28a604508965067c85c5Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Negativesplash10-0006-9000000000-360e0667ff3d7d77e706Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Negativesplash10-0006-9000000000-b1fecd2d1fa166e22d5fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-004i-1920000000-1a2e609b8a19ef491964Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-004i-1900000000-5e4a733641fa285e7f74Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-004i-3900000000-f734d5813fecb7a31814Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-01t9-5900000000-53b0016c66aa014c2abcSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-03e9-9600000000-48f1a0d5512651a93e14Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-004i-1910000000-f02c2133ea475f4f838cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-08i0-2900000000-ec21970768da0fbf8ce5Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0002-9000000000-17c234cb0e8de5ae82f4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-014i-9000000000-d7e5ed251a93758682ecSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-0090000000-435be9f03e969dbabb79Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , negativesplash10-0006-5690000000-79b230d52929aa67bbf2Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-9ad72ff6cb2e2dfab911Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-4900000000-3b1e6c50c2450e123648Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-6900000000-d30b05dfe1b6d25ebd2bSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-052g-1940000000-ce16baa1ceb8a83565c2Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufr-3920000000-c6ff3f238b6fed007635Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-104a4f5a4fe8a0ed5ca3Spectrum
MSMass Spectrum (Electron Ionization)splash10-01dj-9300000000-6e24b5b6d36e07dd73d0Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Toxicity Profile
Route of ExposureNot Available
Mechanism of ToxicityNot Available
MetabolismNot Available
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesThis is an endogenously produced metabolite found in the human body. It is used in metabolic reactions, catabolic reactions or waste generation.
Minimum Risk LevelNot Available
Health EffectsNot Available
SymptomsNot Available
TreatmentNot Available
Concentrations
Not Available
DrugBank IDDB04485
HMDB IDHMDB0000273
FooDB IDFDB031201
Phenol Explorer IDNot Available
KNApSAcK IDC00019698
BiGG ID50348
BioCyc IDTHYMIDINE
METLIN ID3375
PDB IDNot Available
Wikipedia LinkThymidine
Chemspider ID5585
ChEBI ID17748
PubChem Compound ID5789
Kegg Compound IDC00214
YMDB IDYMDB00507
ECMDB IDECMDB00273
References
Synthesis Reference

Jeffrey D. Wilson, “Preparation of 3’azido-3-’-deoxythymidine.” U.S. Patent US4921950, issued October, 1986.

MSDSLink
General References
1. https://www.ncbi.nlm.nih.gov/pubmed/?term=22770225
2. https://www.ncbi.nlm.nih.gov/pubmed/?term=2559771
3. Herdewijn, P.; Kerremans, L.; Wigerinck, P.; Vandendriessche, F.; Van Aerschot, A. Synthesis of thymidine from 5-iodo-2'-deoxyuridine. Tetrahedron Letters (1991), 32(34), 4397-400.
4. 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.
5. Herdewijn, P.; Kerremans, L.; Wigerinck, P.; Vandendriessche, F.; Van Aerschot, A. Synthesis of thymidine from 5-iodo-2'-deoxyuridine. Tetrahedron Letters (1991), 32(34), 4397-400.
6. Zhao R, Zhang S, Hanscom M, Chattopadhyay S, Goldman ID: Loss of reduced folate carrier function and folate depletion result in enhanced pemetrexed inhibition of purine synthesis. Clin Cancer Res. 2005 Feb 1;11(3):1294-301.
7. Robins HI, Tutsch K, Katschinski DM, Jacobson E, Mehta M, Olsen M, Cohen JD, Tiggelaar CL, Arzoomanian RZ, Alberti D, Feierabend C, Wilding G: Phase I trial of intravenous thymidine and carboplatin in patients with advanced cancer. J Clin Oncol. 1999 Sep;17(9):2922-31.
8. Vogel W, Schempp W, Sigwarth I: Comparison of thymidine, fluorodeoxyuridine, hydroxyurea, and methotrexate blocking at the G1/S phase transition of the cell cycle, studied by replication patterns. Hum Genet. 1978 Dec 18;45(2):193-8.
9. Schill WB, Miska W: Possible effects of the kallikrein-kinin system on male reproductive functions. Andrologia. 1992 Mar-Apr;24(2):69-75.
10. Grinlinton FM, Skinner MA, Birchall NM, Tan PL: Gamma delta + T cells from patients with psoriatic and rheumatoid arthritis respond to streptococcal antigen. J Rheumatol. 1993 Jun;20(6):982-7.
11. Schulz CA, Mehta MP, Badie B, McGinn CJ, Robins HI, Hayes L, Chappell R, Volkman J, Binger K, Arzoomanian R, Simon K, Alberti D, Feierabend C, Tutsch KD, Kunugi KA, Wilding G, Kinsella TJ: Continuous 28-day iododeoxyuridine infusion and hyperfractionated accelerated radiotherapy for malignant glioma: a phase I clinical study. Int J Radiat Oncol Biol Phys. 2004 Jul 15;59(4):1107-15.
12. Isoda K, Kim H, Hamamoto Y: A study on the mesothelial cell kinetics in pleural effusions by DNA cytophotometry and autoradiography with tritiated thymidine. Acta Pathol Jpn. 1984 Jul;34(4):775-83.
13. Ashkenazi S, Cleary KR, Pickering LK, Murray BE, Cleary TG: The association of Shiga toxin and other cytotoxins with the neurologic manifestations of shigellosis. J Infect Dis. 1990 May;161(5):961-5.
14. Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7.
15. Abelson HT, Fosburg MT, Beardsley GP, Goorin AM, Gorka C, Link M, Link D: Methotrexate-induced renal impairment: clinical studies and rescue from systemic toxicity with high-dose leucovorin and thymidine. J Clin Oncol. 1983 Mar;1(3):208-16.
16. Svendsen LB, Stener Jorgensen F, Hart Hansen O, Johansen A, Horn T, Larsen JK: Influence of the prostaglandin E1 analogue Rioprostil on the human gastric mucosa. Digestion. 1987;37(1):29-34.