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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2017-12-07 01:19:49 UTC
HMDB IDHMDB0000884
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 ).
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 KeyDWRXFEITVBNRMK-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
  • Glycosyl compound
  • N-glycosyl compound
  • Pentose monosaccharide
  • Pyrimidone
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Vinylogous amide
  • Tetrahydrofuran
  • Heteroaromatic compound
  • 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
Ontology
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 g/LALOGPS
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 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity56.92 m³·mol⁻¹ChemAxon
Polarizability24.02 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
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
NameSMPDB/PathwhizKEGG
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
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
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022298
KNApSAcK IDNot Available
Chemspider ID393058
KEGG Compound IDNot Available
BioCyc IDCPD-15123
BiGG IDNot Available
Wikipedia Link5-methyluridine
METLIN ID5843
PubChem Compound445408
PDB IDNot Available
ChEBI ID45996
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. [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 ]

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