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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-08-24 11:48:54 UTC
Update Date2020-02-26 21:25:14 UTC
HMDB IDHMDB0004813
Secondary Accession Numbers
  • HMDB04813
Metabolite Identification
Common Name3-Methyluridine
Description3-Methyluridine belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety. 5-Methyluridine contains a thymine base joined to a ribose pentose sugar. 3-Methyluridine is an extremely weak basic (essentially neutral) compound (based on its pKa). The chemical compound 5-methyluridine, also called ribothymidine, is a pyrimidine nucleoside. It is the ribonucleoside counterpart to the deoxyribonucleoside thymidine, which lacks a hydroxyl group at the 2' position. The stability of 5-methyluridine under standard temperature and pressure (STP) is very high. It exists in solid form as small white crystals or white crystalline powder, has a molecular weight of 258.23 u, and has a melting point of 185 °C.
Structure
Data?1582752314
Synonyms
ValueSource
3-Methyl-uridineHMDB
N-3-MethyluridineHMDB
N3-MethyluridineHMDB
3-MethyluridineMeSH
Chemical FormulaC10H14N2O6
Average Molecular Weight258.228
Monoisotopic Molecular Weight258.08518619
IUPAC Name1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional NameN-3-methyluridine
CAS Registry Number2140-69-4
SMILES
CN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O
InChI Identifier
InChI=1S/C10H14N2O6/c1-11-6(14)2-3-12(10(11)17)9-8(16)7(15)5(4-13)18-9/h2-3,5,7-9,13,15-16H,4H2,1H3
InChI KeyUTQUILVPBZEHTK-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides 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 ParentsNot Available
SubstituentsNot Available
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location:

Source:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility257 g/LALOGPS
logP-1.4ALOGPS
logP-2.2ChemAxon
logS0ALOGPS
pKa (Strongest Acidic)12.55ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area110.54 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity57.46 m³·mol⁻¹ChemAxon
Polarizability24.21 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-05i3-9420000000-6bfd41e6dad3d99bdefdSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0avr-7869500000-8ecdc253935419deafbbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0920000000-390bf2ef89850c7a98fbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-6900000000-b3415da0734ebf4dd298Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00os-9400000000-12ca095eec130dc54ea9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-6790000000-d0867dbab6597fc7bb3fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a6r-8930000000-0566e352d9e609c17494Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9100000000-7a60aac30d942df68cb4Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not Quantified Not AvailableNot Available
Normal
    details
    UrineDetected but not Quantified Adult (>18 years old)Female
    Normal
    details
    UrineDetected and Quantified0.39 (0.33-0.44) umol/mmol creatinineAdult (>18 years old)BothNormal details
    Abnormal Concentrations
    BiospecimenStatusValueAgeSexConditionReferenceDetails
    UrineDetected but not Quantified Adult (>18 years old)Female
    Ovarian cancer
    details
    Associated Disorders and Diseases
    Disease References
    Ovarian cancer
    1. Woo HM, Kim KM, Choi MH, Jung BH, Lee J, Kong G, Nam SJ, Kim S, Bai SW, Chung BC: Mass spectrometry based metabolomic approaches in urinary biomarker study of women's cancers. Clin Chim Acta. 2009 Feb;400(1-2):63-9. doi: 10.1016/j.cca.2008.10.014. Epub 2008 Oct 30. [PubMed:19010317 ]
    Associated OMIM IDs
    DrugBank IDNot Available
    Phenol Explorer Compound IDNot Available
    FoodDB IDFDB023424
    KNApSAcK IDNot Available
    Chemspider ID280553
    KEGG Compound IDNot Available
    BioCyc IDNot Available
    BiGG IDNot Available
    Wikipedia Link5-Methyluridine
    METLIN ID7077
    PubChem Compound316991
    PDB IDNot Available
    ChEBI ID89487
    Food Biomarker OntologyNot Available
    VMH IDNot Available
    References
    Synthesis ReferenceLevene, P. A.; Tipson, R. Stuart. N-Methyluridine and its bearing on the structure of uridine. Journal of Biological Chemistry (1934), 104 385-93.
    Material Safety Data Sheet (MSDS)Not Available
    General References
    1. Lee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7. [PubMed:15116424 ]
    2. Kammerer B, Frickenschmidt A, Muller CE, Laufer S, Gleiter CH, Liebich H: Mass spectrometric identification of modified urinary nucleosides used as potential biomedical markers by LC-ITMS coupling. Anal Bioanal Chem. 2005 Jun;382(4):1017-26. Epub 2005 May 19. [PubMed:15906010 ]