Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2013-02-09 00:08:13 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 IUPAC 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
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Lysosome
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Cerebrospinal Fluid (CSF)
  • 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
BiofluidStatusValueAgeSexConditionReference
Amniotic FluidDetected and Quantified1.52 +/- 1.21 uMAdult (>18 years old)FemaleNormal
BloodDetected and Quantified0.2 +/- 0.0 uMAdult (>18 years old)BothNormal
BloodDetected and Quantified0.21 +/- 0.13 uMAdult (>18 years old)BothNormal
UrineDetected and Quantified2.46 +/- 2.03 umol/mmol creatinineChildren (1-13 year old)BothNormal
UrineDetected and Quantified1.38 +/- 1.02 umol/mmol creatinineAdolescent (13-18 years old)BothNormal
UrineDetected and Quantified6.87 +/- 4.86 umol/mmol creatinineAdult (>18 years old)BothNormal
UrineDetected and Quantified2.2 (0.7-3.9) umol/mmol creatinineAdult (>18 years old)BothCommentNormal
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReference
BloodDetected and Quantified0.31 +/- 0.09 uMAdult (>18 years old)BothCanavan disease
Cerebrospinal Fluid (CSF)Detected and Quantified0.06 (0.0-0.120 uMAdult (>18 years old)BothDegenerative disc disease
UrineDetected and Quantified4.58 +/- 4.58 umol/mmol creatinineAdult (>18 years old)BothCanavan disease
Associated Disorders and Diseases
Disease References
Canavan disease
  • 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
  • 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)Not Available
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

Gene Name:
NT5E
Uniprot ID:
P21589
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5C1B
Uniprot ID:
Q96P26
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5C1A
Uniprot ID:
Q9BXI3
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5C
Uniprot ID:
Q8TCD5
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5M
Uniprot ID:
Q9NPB1
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5C3
Uniprot ID:
Q9H0P0
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
NT5C2
Uniprot ID:
P49902
Reactions
5-Thymidylic acid + Water unknown Thymidine + Phosphoric aciddetails
Gene Name:
TK1
Uniprot ID:
P04183
Reactions
Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic aciddetails
Gene Name:
TK2
Uniprot ID:
O00142
Reactions
Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic aciddetails
Gene Name:
TYMP
Uniprot ID:
P19971
Reactions
Thymidine + Phosphoric acid unknown Thymine + Deoxyribose 1-phosphatedetails
Gene Name:
Not Available
Uniprot ID:
Q8IZR3

Transporters

Gene Name:
SLC22A1
Uniprot ID:
O15245
Gene Name:
SLC28A3
Uniprot ID:
Q9HAS3