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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2014-10-29 21:49:05 UTC
HMDB IDHMDB00273
Secondary Accession NumbersNone
Metabolite Identification
Common NameThymidine
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.
Structure
Thumb
Synonyms
  1. 1-(2-Deoxy-b-D-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione
  2. 1-(2-Deoxy-beta-delta-erythro-pentofuranosyl)-5-methyl-2,4(1H,3H)-pyrimidinedione
  3. 1-[4-Hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
  4. 2'-Deoxy-5-methyl-Uridine
  5. 2'-Deoxythymidine
  6. 5-Methyl-2'-deoxyuridine
  7. 5-Methyldeoxyuridine
  8. Deoxyribothymidine
  9. Deoxythymidine
  10. DT
  11. DThyd
  12. Thymidin
  13. Thymidine
  14. Thymine 2-desoxyriboside
  15. Thymine deoxyriboside
  16. Thymine-1 2-deoxy-b-D-Ribofuranoside
  17. Thymine-1 2-deoxy-beta-delta-Ribofuranoside
Chemical FormulaC10H14N2O5
Average Molecular Weight242.2286
Monoisotopic Molecular Weight242.090271568
IUPAC Name1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymidine
CAS Registry Number50-89-5
SMILES
CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O
InChI Identifier
InChI=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
KingdomOrganic Compounds
Super ClassNucleosides, Nucleotides, and Analogues
ClassPyrimidine Nucleosides and Analogues
Sub ClassPyrimidine 2'-deoxyribonucleosides and Analogues
Other Descriptors
  • Aromatic Heteropolycyclic Compounds
  • Organic Compounds
  • a deoxynucleoside(Cyc)
  • a pyrimidine-related compound(Cyc)
Substituents
  • Hydropyrimidine
  • Oxolane
  • Primary Alcohol
  • Pyrimidine
  • Pyrimidone
  • Secondary Alcohol
Direct ParentPyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
  • DNA component
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Lysosome
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility73.5 mg/mLNot Available
LogP-0.93SANGSTER (1993)
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 Area99.1ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.41ChemAxon
Polarizability23.06ChemAxon
Spectra
SpectraGC-MSMS/MSLC-MS1D NMR2D NMR
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Lysosome
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Saliva
  • Urine
Tissue Location
  • 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 MetabolismSMP00046map00240
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
Amniotic FluidDetected and Quantified1.52 +/- 1.21 uMAdult (>18 years old)FemaleNormal details
BloodDetected and Quantified0.2 +/- 0.0 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.21 +/- 0.13 uMAdult (>18 years old)BothNormal details
SalivaDetected and Quantified0.221 +/- 0.800 uMAdult (>18 years old)Male
Normal
    • Sugimoto et al. (...
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected and Quantified2.52 +/- 0.579 uMAdult (>18 years old)Female
Normal
    • Sugimoto et al. (...
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
SalivaDetected but not QuantifiedNot ApplicableAdult (>18 years old)Male
Normal
details
UrineDetected and Quantified2.46 +/- 2.03 umol/mmol creatinineChildren (1-13 years old)BothNormal details
UrineDetected and Quantified1.38 +/- 1.02 umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified6.87 +/- 4.86 umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified2.2 (0.7-3.9) umol/mmol creatinineAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.31 +/- 0.09 uMAdult (>18 years old)BothCanavan disease details
Cerebrospinal Fluid (CSF)Detected and Quantified0.06 (0.0-0.120 uMAdult (>18 years old)BothDegenerative disc disease details
UrineDetected and Quantified4.58 +/- 4.58 umol/mmol creatinineAdult (>18 years old)BothCanavan disease details
Associated Disorders and Diseases
Disease References
Canavan disease
  1. Tavazzi B, Lazzarino G, Leone P, Amorini AM, Bellia F, Janson CG, Di Pietro V, Ceccarelli L, Donzelli S, Francis JS, Giardina B: Simultaneous high performance liquid chromatographic separation of purines, pyrimidines, N-acetylated amino acids, and dicarboxylic acids for the chemical diagnosis of inborn errors of metabolism. Clin Biochem. 2005 Nov;38(11):997-1008. Epub 2005 Sep 1. Pubmed: 16139832
Degenerative disc disease
  1. 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. Pubmed: 6656991
Associated OMIM IDs
DrugBank IDDB04485
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB012757
KNApSAcK IDC00019698
Chemspider ID5585
KEGG Compound IDC00214
BioCyc IDTHYMIDINE
BiGG ID50348
Wikipedia LinkThymidine
NuGOwiki LinkHMDB00273
Metagene LinkHMDB00273
METLIN ID3375
PubChem Compound5789
PDB IDTHM
ChEBI ID17748
References
Synthesis ReferenceHerdewijn, 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.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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. Pubmed: 6656991
  2. 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. Pubmed: 15709201
  3. 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. Pubmed: 10561372
  4. 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. Pubmed: 153886
  5. Schill WB, Miska W: Possible effects of the kallikrein-kinin system on male reproductive functions. Andrologia. 1992 Mar-Apr;24(2):69-75. Pubmed: 1318646
  6. 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. Pubmed: 8350335
  7. 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. Pubmed: 15234045
  8. 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. Pubmed: 6485796
  9. 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. Pubmed: 2324546
  10. 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. Pubmed: 6607976
  11. 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. Pubmed: 3111919

Enzymes

General function:
Involved in hydrolase activity
Specific function:
Hydrolyzes extracellular nucleotides into membrane permeable nucleosides.
Gene Name:
NT5E
Uniprot ID:
P21589
Molecular weight:
57948.125
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity).
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Molecular weight:
68803.055
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in nucleotide binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides and has a broad substrate specificity. Helps to regulate adenosine levels in heart during ischemia and hypoxia.
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Molecular weight:
41020.145
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in metal ion binding
Specific function:
Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Molecular weight:
Not Available
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in phosphatase activity
Specific function:
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP.
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Molecular weight:
Not Available
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in magnesium ion binding
Specific function:
Can act both as nucleotidase and as phosphotransferase.
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Molecular weight:
33914.91
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Involved in 5'-nucleotidase activity
Specific function:
May have a critical role in the maintenance of a constant composition of intracellular purine/pyrimidine nucleotides in cooperation with other nucleotidases. Preferentially hydrolyzes inosine 5'-monophosphate (IMP) and other purine nucleotides.
Gene Name:
NT5C2
Uniprot ID:
P49902
Molecular weight:
64969.2
Reactions
5-Thymidylic acid + Water → Thymidine + Phosphoric aciddetails
General function:
Nucleotide transport and metabolism
Specific function:
Not Available
Gene Name:
TK1
Uniprot ID:
P04183
Molecular weight:
25468.455
Reactions
Adenosine triphosphate + Thymidine → ADP + 5-Thymidylic aciddetails
General function:
Involved in ATP binding
Specific function:
Deoxyribonucleoside kinase that phosphorylates thymidine, deoxycytidine, and deoxyuridine. Also phosphorylates anti-viral and anti-cancer nucleoside analogs.
Gene Name:
TK2
Uniprot ID:
O00142
Molecular weight:
27561.495
Reactions
Adenosine triphosphate + Thymidine → ADP + 5-Thymidylic aciddetails
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. Pubmed: 17139284
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. Pubmed: 17016423
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. Pubmed: 10592235
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:
TYMP
Uniprot ID:
P19971
Molecular weight:
49954.965
Reactions
Thymidine + Phosphoric acid → Thymine + Deoxyribose 1-phosphatedetails
General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
Not Available
Uniprot ID:
Q8IZR3
Molecular weight:
35439.6

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)- N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:
SLC22A1
Uniprot ID:
O15245
Molecular weight:
61187.4
References
  1. Zhang L, Dresser MJ, Gray AT, Yost SC, Terashita S, Giacomini KM: Cloning and functional expression of a human liver organic cation transporter. Mol Pharmacol. 1997 Jun;51(6):913-21. Pubmed: 9187257
General function:
Involved in nucleoside:sodium symporter activity
Specific function:
Sodium-dependent, pyrimidine- and purine-selective. Involved in the homeostasis of endogenous nucleosides. Exhibits the transport characteristics of the nucleoside transport system cib or N3 subtype (N3/cib) (with marked transport of both thymidine and inosine). Employs a 2:1 sodium/nucleoside ratio. Also able to transport gemcitabine, 3'-azido-3'-deoxythymidine (AZT), ribavirin and 3-deazauridine
Gene Name:
SLC28A3
Uniprot ID:
Q9HAS3
Molecular weight:
76929.6