You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-10-23 18:27:18 UTC
Secondary Accession Numbers
  • HMDB00884
Metabolite Identification
Common NameRibothymidine
DescriptionRibothymidine is an endogenous methylated nucleoside found in human fluids; methylated purine bases are present in higher amounts in tumor-bearing patients compared to healthy controls.DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents. When chemical bonds to DNA, the DNA becomes damaged and proper and complete replication cannot occur to make the normal intended cell. A DNA adduct is an abnormal piece of DNA covalently-bonded to a cancer-causing chemical. This has shown to be the start of a cancerous cell, or carcinogenesis. DNA adducts in scientific experiments are used as bio-markers and as such are themselves measured to reflect quantitatively, for comparison, the amount of cancer in the subject. (PMID: 3506820 , 17044778 , 17264127 , 16799933 ).
Thymine ribosideChEBI
b-D-Ribofuranoside thymine-1HMDB
beta-delta-Ribofuranoside thymine-1HMDB
Thymine ribofuranosideHMDB
Thymine ribonucleosideHMDB
Thymine-1 beta-D-ribofuranosylthymineHMDB
Thymine-1 beta-delta-ribofuranosylthymineHMDB
Chemical FormulaC10H14N2O6
Average Molecular Weight258.228
Monoisotopic Molecular Weight258.08518619
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Namethymidin
CAS Registry Number1463-10-1
InChI Identifier
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleosides
Direct ParentPyrimidine nucleosides
Alternative Parents
  • Pyrimidine nucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Vinylogous amide
  • Heteroaromatic compound
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • Organoheterocyclic compound
  • Oxacycle
  • Azacycle
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Primary alcohol
  • Alcohol
  • Organic oxygen compound
  • Organic oxide
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors

Biological Location:


  Biofluid and excreta:


Physical Properties
Experimental Properties
Melting Point183 - 187 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility135 g/LALOGPS
pKa (Strongest Acidic)9.95ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity56.92 m³·mol⁻¹ChemAxon
Polarizability24.02 ųChemAxon
Number of Rings2ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05bf-9420000000-897dab8f4bbf7b8e664cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0kp0-6879400000-656a0a43be4a2cd044e7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-004i-0900000000-1653ad80c56ae3727f92View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-004i-2900000000-826774188d3e78ca38f2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0a6r-9800000000-f5daf31a98b364b70f8cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0910000000-90f6da130f49fa9df29dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-5900000000-203a4367756530615ffdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004j-9800000000-13e51659da01285bdc7fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a6r-1490000000-4ba707a2228996f9f9f7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-6920000000-a25c60ade61d6d32f0f1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-001m-9100000000-37e601ae2d82d72111e7View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Feces
  • Urine
Tissue LocationNot Available
PathwaysNot Available
No entries found
Normal Concentrations
BloodDetected and Quantified0.200 +/- 0.098 uMAdult (>18 years old)Not SpecifiedNormal
    • Xu, G., Enderle, ...
UrineDetected and Quantified0.28 +/- 0.17 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
FecesDetected but not Quantified Adult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified0.51 +/- 0.53 umol/mmol creatinineAdult (>18 years old)BothBreast cancer details
Associated Disorders and Diseases
Disease References
Perillyl alcohol administration for cancer treatment
  1. Zheng YF, Kong HW, Xiong JH, Lv S, Xu GW: Clinical significance and prognostic value of urinary nucleosides in breast cancer patients. Clin Biochem. 2005 Jan;38(1):24-30. [PubMed:15607313 ]
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB022298
KNApSAcK IDNot Available
Chemspider ID393058
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link5-Methyluridine
PubChem Compound445408
PDB IDNot Available
ChEBI ID30821
Synthesis ReferenceMaruyama, Shogo; Kumon, Satoru. 5-Methyluridine manufacture with microorganism. Jpn. Kokai Tokkyo Koho (1996), 6 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Avraham Y, Grossowicz N, Yashphe J: Purification and characterization of uridine and thymidine phosphorylase from Lactobacillus casei. Biochim Biophys Acta. 1990 Sep 3;1040(2):287-93. [PubMed:2119230 ]
  2. Lang TT, Selner M, Young JD, Cass CE: Acquisition of human concentrative nucleoside transporter 2 (hcnt2) activity by gene transfer confers sensitivity to fluoropyrimidine nucleosides in drug-resistant leukemia cells. Mol Pharmacol. 2001 Nov;60(5):1143-52. [PubMed:11641443 ]
  3. Urbonavicius J, Durand JM, Bjork GR: Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri. J Bacteriol. 2002 Oct;184(19):5348-57. [PubMed:12218021 ]
  4. Hacia JG, Woski SA, Fidanza J, Edgemon K, Hunt N, McGall G, Fodor SP, Collins FS: Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates. Nucleic Acids Res. 1998 Nov 1;26(21):4975-82. [PubMed:9776762 ]
  5. Mori T, Guo MW, Li X, Xu JP, Mori E: Isolation and identification of apoptosis inducing nucleosides from CD57(+)HLA-DRbright natural suppressor cell line. Biochem Biophys Res Commun. 1998 Oct 20;251(2):416-22. [PubMed:9792789 ]
  6. Weisbart RH, Garrett RA, Liebling MR, Barnett EV, Paulus HE, Katz DH: Specificity of anti-nucleoside antibodies in systemic lupus erythematosus. Clin Immunol Immunopathol. 1983 Jun;27(3):403-11. [PubMed:6603316 ]
  7. Morris GS, Simmonds HA, Davies PM: Use of biological fluids for the rapid diagnosis of potentially lethal inherited disorders of human purine and pyrimidine metabolism. Biomed Chromatogr. 1986 Jun;1(3):109-18. [PubMed:3506820 ]
  8. Cho SH, Jung BH, Lee SH, Lee WY, Kong G, Chung BC: Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography-tandem mass spectrometry. Biomed Chromatogr. 2006 Nov;20(11):1229-36. [PubMed:16799933 ]
  9. Yang TH, Hu ML: Intracellular levels of S-adenosylhomocysteine but not homocysteine are highly correlated to the expression of nm23-H1 and the level of 5-methyldeoxycytidine in human hepatoma cells with different invasion activities. Nutr Cancer. 2006;55(2):224-31. [PubMed:17044778 ]
  10. Liu Z, Liu S, Xie Z, Blum W, Perrotti D, Paschka P, Klisovic R, Byrd J, Chan KK, Marcucci G: Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method. Nucleic Acids Res. 2007;35(5):e31. Epub 2007 Jan 30. [PubMed:17264127 ]


General function:
Involved in RNA methyltransferase activity
Specific function:
Probable S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNA. May also have a role in tRNA stabilization or maturation (By similarity).
Gene Name:
Uniprot ID:
Molecular weight: