Human Metabolome Database Version 3.5

Showing metabocard for Thymidine (HMDB00273)

Record Information
Version 3.5
Creation Date 2005-11-16 08:48:42 -0700
Update Date 2013-02-08 17:08:13 -0700
HMDB ID HMDB00273
Secondary Accession Numbers None
Metabolite Identification
Common Name Thymidine
Description Thymidine 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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
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 Formula C10H14N2O5
Average Molecular Weight 242.2286
Monoisotopic Molecular Weight 242.090271568
IUPAC Name 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional IUPAC Name thymidine
CAS Registry Number 50-89-5
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 Key IQFYYKKMVGJFEH-XLPZGREQSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Nucleosides, Nucleotides, and Analogues
Class Pyrimidine Nucleosides and Analogues
Sub Class Pyrimidine 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 Parent Pyrimidine 2'-deoxyribonucleosides and Analogues
Ontology
Status Detected and Quantified
Origin
  • Endogenous
Biofunction
  • Component of Purine metabolism
  • Component of Pyrimidine metabolism
  • DNA component
Application Not Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Lysosome
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility 73.5 mg/mL Not Available
LogP -0.93 SANGSTER (1993)
Predicted Properties
Property Value Source
Water Solubility 66.8 g/L ALOGPS
LogP -1.32 ALOGPS
LogP -1.1 ChemAxon
LogS -0.56 ALOGPS
pKa (strongest acidic) 9.96 ChemAxon
pKa (strongest basic) -3 ChemAxon
Hydrogen Acceptor Count 5 ChemAxon
Hydrogen Donor Count 3 ChemAxon
Polar Surface Area 99.1 A2 ChemAxon
Rotatable Bond Count 2 ChemAxon
Refractivity 55.41 ChemAxon
Polarizability 23.06 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 0 ChemAxon
Spectra
1H NMR Spectrum
MS/MS Spectrum Quattro_QQQ 10
MS/MS Spectrum Quattro_QQQ 25
MS/MS Spectrum Quattro_QQQ 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 10
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 20
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 30
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 40
MS/MS Spectrum LC-ESI-QQ (API3000, Applied Biosystems) 50
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
MS/MS Spectrum LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies)
[1H,1H] 2D NMR Spectrum
[1H,13C] 2D NMR Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Lysosome
Biofluid Locations
  • Amniotic Fluid
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue Location
  • Muscle
  • Skeletal Muscle
  • Bladder
  • Fibroblasts
  • Intestine
  • Neuron
  • Pancreas
  • Placenta
  • Testes
  • Kidney
  • Thyroid Gland
  • Prostate
  • Adrenal Gland
  • Fetus
  • Skin
  • Adipose Tissue
  • Platelet
  • Spleen
  • Stratum Corneum
Pathways
Name SMPDB Link KEGG Link
Pyrimidine Metabolism SMP00046 map00240 Link_out
Normal Concentrations
Biofluid Status Value Age Sex Condition Reference
Amniotic Fluid Detected and Quantified
1.52 +/- 1.21 uM Adult (>18 years old) Female Normal
Blood Detected and Quantified
0.2 +/- 0.0 uM Adult (>18 years old) Both Normal
Blood Detected and Quantified
0.21 +/- 0.13 uM Adult (>18 years old) Both Normal
Urine Detected and Quantified
2.46 +/- 2.03 umol/mmol creatinine Children (1-13 year old) Both Normal
Urine Detected and Quantified
1.38 +/- 1.02 umol/mmol creatinine Adolescent (13-18 years old) Both Normal
Urine Detected and Quantified
6.87 +/- 4.86 umol/mmol creatinine Adult (>18 years old) Both Normal
Urine Detected and Quantified
2.2 (0.7-3.9) umol/mmol creatinine Adult (>18 years old) Both Comment Normal
Abnormal Concentrations
Biofluid Status Value Age Sex Condition Reference
Blood Detected and Quantified 0.31 +/- 0.09 uM Adult (>18 years old) Both Canavan disease
Cerebrospinal Fluid (CSF) Detected and Quantified 0.06 (0.0-0.120 uM Adult (>18 years old) Both Degenerative disc disease
Urine Detected and Quantified 4.58 +/- 4.58 umol/mmol creatinine Adult (>18 years old) Both Canavan disease
Associated Disorders and Diseases
Disease References
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 Link_out
      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 Link_out
          Associated OMIM IDs
          DrugBank ID DB04485 Link_out
          DrugBank Metabolite ID Not Available
          Phenol Explorer Compound ID Not Available
          Phenol Explorer Metabolite ID Not Available
          FoodDB ID FDB012757
          KNApSAcK ID C00019698 Link_out
          Chemspider ID 5585 Link_out
          KEGG Compound ID C00214 Link_out
          BioCyc ID THYMIDINE Link_out
          BiGG ID 50348 Link_out
          Wikipedia Link Thymidine Link_out
          NuGOwiki Link HMDB00273 Link_out
          Metagene Link HMDB00273 Link_out
          METLIN ID 3375 Link_out
          PubChem Compound 5789 Link_out
          PDB ID THM Link_out
          ChEBI ID 17748 Link_out
          References
          Synthesis Reference 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.
          Material Safety Data Sheet (MSDS) Download (PDF)
          General References
          1. 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 Link_out
          2. 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 Link_out
          3. 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 Link_out
          4. 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 Link_out
          5. 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 Link_out
          6. 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 Link_out
          7. 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 Link_out
          8. 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 Link_out
          9. 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 Link_out
          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 Link_out
          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 Link_out

          Enzymes
          Name: 5'-nucleotidase
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5E
          Uniprot ID: P21589 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Cytosolic 5'-nucleotidase 1B
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5C1B
          Uniprot ID: Q96P26 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Cytosolic 5'-nucleotidase 1A
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5C1A
          Uniprot ID: Q9BXI3 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: 5'(3')-deoxyribonucleotidase, cytosolic type
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5C
          Uniprot ID: Q8TCD5 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: 5'(3')-deoxyribonucleotidase, mitochondrial
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5M
          Uniprot ID: Q9NPB1 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Cytosolic 5'-nucleotidase 3
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5C3
          Uniprot ID: Q9H0P0 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Cytosolic purine 5'-nucleotidase
          Reactions:
          5-Thymidylic acid + Water unknown Thymidine + Phosphoric acid details
          Gene Name: NT5C2
          Uniprot ID: P49902 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Thymidine kinase, cytosolic
          Reactions:
          Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic acid details
          Gene Name: TK1
          Uniprot ID: P04183 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Thymidine kinase 2, mitochondrial
          Reactions:
          Adenosine triphosphate + Thymidine unknown ADP + 5-Thymidylic acid details
          Gene Name: TK2
          Uniprot ID: O00142 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Thymidine phosphorylase
          Reactions:
          Thymidine + Phosphoric acid unknown Thymine + Deoxyribose 1-phosphate details
          Gene Name: TYMP
          Uniprot ID: P19971 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Thymidine kinase
          Reactions: Not Available
          Gene Name: Not Available
          Uniprot ID: Q8IZR3 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Transporters
          Name: Solute carrier family 22 member 1
          Reactions: Not Available
          Gene Name: SLC22A1
          Uniprot ID: O15245 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA
          Name: Solute carrier family 28 member 3
          Reactions: Not Available
          Gene Name: SLC28A3
          Uniprot ID: Q9HAS3 Link_out
          Protein Sequence: FASTA
          Gene Sequence: FASTA