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Record Information
Version4.0
Creation Date2006-08-24 11:48:54 UTC
Update Date2017-09-25 09:32:13 UTC
HMDB IDHMDB0004813
Secondary Accession Numbers
  • HMDB04813
StatusDetected and Quantified
Metabolite Identification
Common Name3-Methyluridine
Description3-Methyluridine is a modified nucleoside of cellular RNA. All modifications are formed post-transcriptionally in RNA from the normal nucleosides by modifying enzymes, especially specific RNA-methyltransferases and RNA-synthetases. Due to the lack of specific phosphorylases for modified nucleosides they cannot be recycled for synthesizing RNA, so they are excreted quantitatively in urine. (PMID 15906010 ).
Structure
Thumb
Synonyms
ValueSource
3-Methyl-uridineHMDB
N-3-MethyluridineHMDB
N3-MethyluridineHMDB
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
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
Substituents
  • 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 DescriptorsNot Available
Ontology
Disposition
Biological Location:
Source:
Biofluid and excreta:
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 Solubility257.0 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity57.46 m3·mol-1ChemAxon
Polarizability24.21 Å3ChemAxon
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-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
No entries found
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
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
    BiofluidStatusValueAgeSexConditionReferenceDetails
    UrineDetected but not Quantified Adult (>18 years old)Female
    Ovarian cancer
    details
    Associated Disorders and Diseases
    Disease ReferencesNone
    Associated OMIM IDsNone
    DrugBank IDNot Available
    DrugBank Metabolite IDNot Available
    Phenol Explorer Compound IDNot Available
    Phenol Explorer Metabolite IDNot Available
    FoodDB IDFDB023424
    KNApSAcK IDNot Available
    Chemspider ID280553
    KEGG Compound IDNot Available
    BioCyc IDNot Available
    BiGG IDNot Available
    Wikipedia LinkNot Available
    NuGOwiki LinkHMDB0004813
    METLIN ID7077
    PubChem Compound316991
    PDB IDNot Available
    ChEBI ID89487
    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 ]