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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-24 11:48:54 UTC
Update Date2021-09-14 15:47:57 UTC
HMDB IDHMDB0004813
Secondary Accession Numbers
  • HMDB04813
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
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 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 DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg166.83930932474
Predicted Molecular 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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+158.81331661259
DarkChem[M-H]-156.73631661259
DeepCCS[M+H]+155.64830932474
DeepCCS[M-H]-153.2930932474
DeepCCS[M-2H]-187.0130932474
DeepCCS[M+Na]+161.92730932474
AllCCS[M+H]+158.132859911
AllCCS[M+H-H2O]+154.432859911
AllCCS[M+NH4]+161.532859911
AllCCS[M+Na]+162.532859911
AllCCS[M-H]-156.532859911
AllCCS[M+Na-2H]-156.532859911
AllCCS[M+HCOO]-156.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-MethyluridineCN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O3199.5Standard polar33892256
3-MethyluridineCN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O1885.5Standard non polar33892256
3-MethyluridineCN1C(=O)C=CN(C2OC(CO)C(O)C2O)C1=O2323.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Methyluridine,1TMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O)C2O)C1=O2466.9Semi standard non polar33892256
3-Methyluridine,1TMS,isomer #2CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C)C2O)C1=O2501.0Semi standard non polar33892256
3-Methyluridine,1TMS,isomer #3CN1C(=O)C=CN(C2OC(CO)C(O)C2O[Si](C)(C)C)C1=O2490.1Semi standard non polar33892256
3-Methyluridine,2TMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O)C1=O2497.5Semi standard non polar33892256
3-Methyluridine,2TMS,isomer #2CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O)C2O[Si](C)(C)C)C1=O2501.2Semi standard non polar33892256
3-Methyluridine,2TMS,isomer #3CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C1=O2485.0Semi standard non polar33892256
3-Methyluridine,3TMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C)C(O[Si](C)(C)C)C2O[Si](C)(C)C)C1=O2466.3Semi standard non polar33892256
3-Methyluridine,1TBDMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O)C2O)C1=O2772.1Semi standard non polar33892256
3-Methyluridine,1TBDMS,isomer #2CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C(C)(C)C)C2O)C1=O2767.0Semi standard non polar33892256
3-Methyluridine,1TBDMS,isomer #3CN1C(=O)C=CN(C2OC(CO)C(O)C2O[Si](C)(C)C(C)(C)C)C1=O2766.0Semi standard non polar33892256
3-Methyluridine,2TBDMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O)C1=O3000.0Semi standard non polar33892256
3-Methyluridine,2TBDMS,isomer #2CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O)C2O[Si](C)(C)C(C)(C)C)C1=O2991.6Semi standard non polar33892256
3-Methyluridine,2TBDMS,isomer #3CN1C(=O)C=CN(C2OC(CO)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C1=O2969.0Semi standard non polar33892256
3-Methyluridine,3TBDMS,isomer #1CN1C(=O)C=CN(C2OC(CO[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C2O[Si](C)(C)C(C)(C)C)C1=O3196.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methyluridine GC-MS (Non-derivatized) - 70eV, Positivesplash10-05i3-9420000000-6bfd41e6dad3d99bdefd2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methyluridine GC-MS (3 TMS) - 70eV, Positivesplash10-0avr-7869500000-8ecdc253935419deafbb2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methyluridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methyluridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Positive-QTOFsplash10-004i-0920000000-390bf2ef89850c7a98fb2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Positive-QTOFsplash10-004i-6900000000-b3415da0734ebf4dd2982016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Positive-QTOFsplash10-00os-9400000000-12ca095eec130dc54ea92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Negative-QTOFsplash10-0a4i-6790000000-d0867dbab6597fc7bb3f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Negative-QTOFsplash10-0a6r-8930000000-0566e352d9e609c174942016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Negative-QTOFsplash10-0006-9100000000-7a60aac30d942df68cb42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Negative-QTOFsplash10-00or-2900000000-4fc534f0dece372189392021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Negative-QTOFsplash10-02dr-4900000000-cf65f9e10d55af99c9842021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Negative-QTOFsplash10-014m-9100000000-4e419ba43aeba839b0272021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 10V, Positive-QTOFsplash10-004i-2900000000-68e7cf8708827caffc0a2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 20V, Positive-QTOFsplash10-004i-5900000000-a4a25fd5fc204c9e85a42021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methyluridine 40V, Positive-QTOFsplash10-004i-7900000000-e0953d880cd7c41bd4e82021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
details
UrineDetected but not QuantifiedNot QuantifiedAdult (>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 QuantifiedNot QuantifiedAdult (>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
FooDB 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
MarkerDB IDNot Available
Good Scents 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 ]