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Record Information
Version3.6
Creation Date2005-11-16 15:48:42 UTC
Update Date2016-02-11 01:03:29 UTC
HMDB IDHMDB00884
Secondary Accession NumbersNone
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 ).
Structure
Thumb
Synonyms
ValueSource
1-(beta-D-Ribofuranosyl)thymineChEBI
RibosylthymidineChEBI
tChEBI
Thymine ribosideChEBI
1-(b-D-Ribofuranosyl)thymineGenerator
1-(β-D-ribofuranosyl)thymineGenerator
1-b-D-RibofuranosylthymineHMDB
1-beta-delta-RibofuranosylthymineHMDB
5-Methyl-1-beta-D-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Methyl-1-beta-delta-ribofuranosyl-2,4(1H,3H)-pyrimidinedioneHMDB
5-Methyl-uridineHMDB
5-MethyluridineHMDB
b-D-Ribofuranoside thymine-1HMDB
beta-D-RibofuranosideHMDB
beta-delta-RibofuranosideHMDB
beta-delta-Ribofuranoside thymine-1HMDB
RibosylthymineHMDB
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
SMILES
CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C(=O)NC1=O
InChI Identifier
InChI=1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1
InChI KeyInChIKey=DWRXFEITVBNRMK-JXOAFFINSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Pyrimidone
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Secondary alcohol
  • Lactam
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
Biofunction
  • Protein component
ApplicationNot Available
Cellular locations
  • Cytoplasm
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point183 - 187 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility135.0 mg/mLALOGPS
logP-1.7ALOGPS
logP-2ChemAxon
logS-0.28ALOGPS
pKa (Strongest Acidic)9.95ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area119.33 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity56.92 m3·mol-1ChemAxon
Polarizability24.02 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
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
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Cytoplasm
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.200 +/- 0.098 uMAdult (>18 years old)Not SpecifiedNormal
    • Xu, G., Enderle, ...
details
UrineDetected and Quantified0.28 +/- 0.17 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
Abnormal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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. [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
NuGOwiki LinkHMDB00884
Metagene LinkHMDB00884
METLIN ID5843
PubChem Compound445408
PDB IDNot Available
ChEBI ID30821
References
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. [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. [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. [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. [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. [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. [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. [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. [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. [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. [17264127 ]

Enzymes

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:
TRMT2B
Uniprot ID:
Q96GJ1
Molecular weight:
56475.965