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Record Information
Version3.6
Creation Date2006-08-24 11:48:54 UTC
Update Date2016-02-11 01:06:51 UTC
HMDB IDHMDB04813
Secondary Accession NumbersNone
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 KeyInChIKey=UTQUILVPBZEHTK-UHFFFAOYSA-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
  • Saccharide
  • 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 DescriptorsNot Available
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
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
SpectraNot Available
Biological Properties
Cellular LocationsNot Available
Biofluid Locations
  • Blood
  • Urine
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
BiofluidStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot ApplicableNot AvailableNot Available
Normal
  • Not Applicable
details
UrineDetected but not QuantifiedNot ApplicableAdult (>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 QuantifiedNot ApplicableAdult (>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 LinkHMDB04813
Metagene LinkHMDB04813
METLIN ID7077
PubChem Compound316991
PDB IDNot Available
ChEBI 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. [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. [15906010 ]