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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2019-04-04 16:06:50 UTC
Update Date2022-09-22 17:44:59 UTC
HMDB IDHMDB0240328
Secondary Accession NumbersNone
Metabolite Identification
Common Name2'-O-Methyluridine
Description2'-O-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. 2'-O-Methyluridine was identified as one of forty plasma metabolites that could be used to predict gut microbiome Shannon diversity (PMID: 31477923 ). Shannon diversity is a metric that summarizes both species abundance and evenness, and it has been suggested as a marker for microbiome health.
Structure
Data?1580829343
Synonyms
ValueSource
O(2')-MethyluridineChEBI
umChEBI
2’-O-methyluridineHMDB
O-MethyluridineHMDB
2'-O-MethyluridineHMDB
Chemical FormulaC10H14N2O6
Average Molecular Weight258.23
Monoisotopic Molecular Weight258.085186179
IUPAC Name1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dione
Traditional Name1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-3H-pyrimidine-2,4-dione
CAS Registry Number2140-76-3
SMILES
CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O
InChI Identifier
InChI=1S/C10H14N2O6/c1-17-8-7(15)5(4-13)18-9(8)12-3-2-6(14)11-10(12)16/h2-3,5,7-9,13,15H,4H2,1H3,(H,11,14,16)/t5-,7-,8-,9-/m1/s1
InChI KeySXUXMRMBWZCMEN-ZOQUXTDFSA-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
  • Pyrimidone
  • Hydroxypyrimidine
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Tetrahydrofuran
  • Heteroaromatic compound
  • Secondary alcohol
  • Azacycle
  • Organoheterocyclic compound
  • Dialkyl ether
  • Oxacycle
  • Ether
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Organic oxygen compound
  • Organic nitrogen compound
  • Primary alcohol
  • Organopnictogen compound
  • Organic oxide
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.4ALOGPS
logP-1.8ChemAxon
logS-0.38ALOGPS
pKa (Strongest Acidic)9.7ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area108.33 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity57.32 m³·mol⁻¹ChemAxon
Polarizability23.91 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
DeepCCS[M+H]+163.69330932474
DeepCCS[M-H]-161.32330932474
DeepCCS[M-2H]-194.9330932474
DeepCCS[M+Na]+170.15630932474
AllCCS[M+H]+158.132859911
AllCCS[M+H-H2O]+154.532859911
AllCCS[M+NH4]+161.632859911
AllCCS[M+Na]+162.532859911
AllCCS[M-H]-156.632859911
AllCCS[M+Na-2H]-156.632859911
AllCCS[M+HCOO]-156.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2'-O-MethyluridineCO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O3241.2Standard polar33892256
2'-O-MethyluridineCO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O2146.5Standard non polar33892256
2'-O-MethyluridineCO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)NC1=O2451.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2'-O-Methyluridine,1TMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)[NH]C1=O2297.4Semi standard non polar33892256
2'-O-Methyluridine,1TMS,isomer #2CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O2279.6Semi standard non polar33892256
2'-O-Methyluridine,1TMS,isomer #3CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2331.5Semi standard non polar33892256
2'-O-Methyluridine,2TMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O2283.3Semi standard non polar33892256
2'-O-Methyluridine,2TMS,isomer #2CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2356.5Semi standard non polar33892256
2'-O-Methyluridine,2TMS,isomer #3CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2365.6Semi standard non polar33892256
2'-O-Methyluridine,3TMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2387.7Semi standard non polar33892256
2'-O-Methyluridine,3TMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2574.1Standard non polar33892256
2'-O-Methyluridine,3TMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C)[C@@H](CO[Si](C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C)C1=O2623.2Standard polar33892256
2'-O-Methyluridine,1TBDMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)[NH]C1=O2514.6Semi standard non polar33892256
2'-O-Methyluridine,1TBDMS,isomer #2CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O2524.9Semi standard non polar33892256
2'-O-Methyluridine,1TBDMS,isomer #3CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O2566.5Semi standard non polar33892256
2'-O-Methyluridine,2TBDMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)[NH]C1=O2731.6Semi standard non polar33892256
2'-O-Methyluridine,2TBDMS,isomer #2CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O2796.0Semi standard non polar33892256
2'-O-Methyluridine,2TBDMS,isomer #3CO[C@@H]1[C@H](O)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O2803.1Semi standard non polar33892256
2'-O-Methyluridine,3TBDMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O3012.1Semi standard non polar33892256
2'-O-Methyluridine,3TBDMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O3139.9Standard non polar33892256
2'-O-Methyluridine,3TBDMS,isomer #1CO[C@@H]1[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO[Si](C)(C)C(C)(C)C)O[C@H]1N1C=CC(=O)N([Si](C)(C)C(C)(C)C)C1=O2946.6Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2'-O-Methyluridine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - 2'-O-Methyluridine 35V, Negative-QTOFsplash10-01ox-8190000000-04836f429bee6438aec52021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 2'-O-Methyluridine 35V, Positive-QTOFsplash10-004i-0900000000-a95dcd4a4fad1b7c10a42021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 10V, Positive-QTOFsplash10-0400-0910000000-90907a6ba444cc94d8052021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 20V, Positive-QTOFsplash10-03di-5900000000-dbfce876c5243b99fa592021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 40V, Positive-QTOFsplash10-0296-9300000000-d997d0b3fefede5e7b642021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 10V, Negative-QTOFsplash10-03di-2920000000-ab0a3d06c2a5fab925222021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 20V, Negative-QTOFsplash10-01ox-9700000000-2ea5d2f1349adb3f0aff2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2'-O-Methyluridine 40V, Negative-QTOFsplash10-0006-9100000000-a6372c939a9cb283f7742021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID92343
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound102212
PDB IDNot Available
ChEBI ID19227
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Wilmanski T, Rappaport N, Earls JC, Magis AT, Manor O, Lovejoy J, Omenn GS, Hood L, Gibbons SM, Price ND: Blood metabolome predicts gut microbiome alpha-diversity in humans. Nat Biotechnol. 2019 Oct;37(10):1217-1228. doi: 10.1038/s41587-019-0233-9. Epub 2019 Sep 2. [PubMed:31477923 ]

Only showing the first 10 proteins. There are 16 proteins in total.

Enzymes

General function:
Involved in methyltransferase activity
Specific function:
Probable methyltransferase.
Gene Name:
FTSJ2
Uniprot ID:
Q9UI43
Molecular weight:
27423.365
General function:
Not Available
Specific function:
Probable adenosyl-L-methionine (AdoMet)-dependent tRNA (uracil-O(2)-)-methyltransferase (By similarity).
Gene Name:
TRMT44
Uniprot ID:
Q8IYL2
Molecular weight:
84628.16
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q2NHD6
Molecular weight:
23393.735
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
A1AG82
Molecular weight:
23334.92
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q2GGT6
Molecular weight:
24373.735
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q2GDL7
Molecular weight:
24052.61
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q6G0S9
Molecular weight:
26685.75
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q6G4Z3
Molecular weight:
27322.35
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q5PLC1
Molecular weight:
23251.825
General function:
Not Available
Specific function:
Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit.
Gene Name:
RLME
Uniprot ID:
Q0BT08
Molecular weight:
24550.145

Only showing the first 10 proteins. There are 16 proteins in total.