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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:45:39 UTC
HMDB IDHMDB0001087
Secondary Accession Numbers
  • HMDB01087
Metabolite Identification
Common Name5-Methylthioribose
Description5-Methylthioribose (CAS: 23656-67-9) belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. 5-Methylthioribose is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Methylthioribose exists in all living organisms, ranging from bacteria to humans. In humans, 5-methylthioribose is involved in the metabolic disorder called hypermethioninemia. Outside of the human body, 5-methylthioribose has been detected, but not quantified in, several different foods, such as alaska wild rhubarbs, common verbena, greenthread tea, pasta, and Irish moss. This could make 5-methylthioribose a potential biomarker for the consumption of these foods. 5-Methylthioribose is a metabolite of 5-methylthioribose-1-phosphate. It is a substrate of methylthioribose kinase (EC 2.7.1.100) in the methionine metabolism pathway (KEGG). It can be found in Escherichia (PMID: 4203512 ).
Structure
Data?1583183618
Synonyms
ValueSource
S-Methyl-5-thio-D-riboseKegg
5-(Methylsulfanyl)-D-riboseKegg
5-(Methylsulphanyl)-D-riboseGenerator
5-Deoxy-5-(methylthio)riboseHMDB
5-Methylthio-D-riboseHMDB
S(5)-Methyl-5-thio-D-riboseHMDB
S5-Methyl-5-thio-D-riboseHMDB
5-MethylthioriboseHMDB
5-S-Methyl-5-thio-D-riboseHMDB
5-S-Methyl-5-thio-beta-D-ribofuranoseHMDB
5-S-Methyl-5-thio-β-D-ribofuranoseHMDB
S-Methyl-5-thio-D-ribofuranoseHMDB
Chemical FormulaC6H12O4S
Average Molecular Weight180.222
Monoisotopic Molecular Weight180.045629562
IUPAC Name(2R,3R,4S,5S)-5-[(methylsulfanyl)methyl]oxolane-2,3,4-triol
Traditional Name5-methylthio-D-ribose
CAS Registry Number624740-12-1
SMILES
CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C6H12O4S/c1-11-2-3-4(7)5(8)6(9)10-3/h3-9H,2H2,1H3/t3-,4-,5-,6-/m1/s1
InChI KeyOLVVOVIFTBSBBH-KVTDHHQDSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Polyol
  • Hydrocarbon derivative
  • Organosulfur compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
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
Water Solubility176 g/LALOGPS
logP10(-1.4) g/LALOGPS
logP10(-0.82) g/LChemAxon
logS10(-0.01) g/LALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.92 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity40.79 m³·mol⁻¹ChemAxon
Polarizability17.67 ųChemAxon
Number of Rings1ChemAxon
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]+142.07531661259
DarkChem[M-H]-138.39331661259
AllCCS[M+H]+140.02932859911
AllCCS[M-H]-137.76332859911
DeepCCS[M+H]+140.98930932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-MethylthioriboseCSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O2964.6Standard polar33892256
5-MethylthioriboseCSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O1560.8Standard non polar33892256
5-MethylthioriboseCSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O1512.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Methylthioribose,1TMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C)[C@H](O)[C@@H]1O1567.5Semi standard non polar33892256
5-Methylthioribose,1TMS,isomer #2CSC[C@H]1O[C@@H](O)[C@H](O[Si](C)(C)C)[C@@H]1O1576.9Semi standard non polar33892256
5-Methylthioribose,1TMS,isomer #3CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O[Si](C)(C)C1557.0Semi standard non polar33892256
5-Methylthioribose,2TMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O1636.4Semi standard non polar33892256
5-Methylthioribose,2TMS,isomer #2CSC[C@H]1O[C@@H](O[Si](C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C1633.8Semi standard non polar33892256
5-Methylthioribose,2TMS,isomer #3CSC[C@H]1O[C@@H](O)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1634.5Semi standard non polar33892256
5-Methylthioribose,3TMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1654.3Semi standard non polar33892256
5-Methylthioribose,1TBDMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O1807.4Semi standard non polar33892256
5-Methylthioribose,1TBDMS,isomer #2CSC[C@H]1O[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O1829.7Semi standard non polar33892256
5-Methylthioribose,1TBDMS,isomer #3CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C1809.8Semi standard non polar33892256
5-Methylthioribose,2TBDMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2130.7Semi standard non polar33892256
5-Methylthioribose,2TBDMS,isomer #2CSC[C@H]1O[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2136.9Semi standard non polar33892256
5-Methylthioribose,2TBDMS,isomer #3CSC[C@H]1O[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2147.1Semi standard non polar33892256
5-Methylthioribose,3TBDMS,isomer #1CSC[C@H]1O[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2400.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methylthioribose GC-MS (Non-derivatized) - 70eV, Positivesplash10-0nor-9600000000-757c4b3ed6add1bdc1682017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methylthioribose GC-MS (3 TMS) - 70eV, Positivesplash10-0719-9247000000-321d54ddf2f38682b57c2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Methylthioribose 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 - 5-Methylthioribose 10V, Positive-QTOFsplash10-001i-0900000000-7914d8991b0a6af1d99f2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 20V, Positive-QTOFsplash10-02ai-2900000000-e36191d55523024bf6432015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 40V, Positive-QTOFsplash10-0bvj-9500000000-94cbb1e527c7c7e213142015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 10V, Negative-QTOFsplash10-0002-9200000000-21073f76322842d53a462015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 20V, Negative-QTOFsplash10-0002-9300000000-89d811f24fdb17e739e82015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 40V, Negative-QTOFsplash10-0002-9000000000-ed328bd35b3fe14404502015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 10V, Negative-QTOFsplash10-004i-1900000000-aefd2630eb3d70da82002021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 20V, Negative-QTOFsplash10-0002-9100000000-57ad8e0e93b83006dc3c2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 40V, Negative-QTOFsplash10-0002-9000000000-789718691297aaebb3ad2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 10V, Positive-QTOFsplash10-01qa-4900000000-1a70ce18540d6a0916d82021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 20V, Positive-QTOFsplash10-03di-8900000000-ca12a9fcff10da6223832021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Methylthioribose 40V, Positive-QTOFsplash10-03dj-9000000000-e18a37fac06996f6a6602021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022418
KNApSAcK IDNot Available
Chemspider ID388938
KEGG Compound IDC03089
BioCyc IDCPD-560
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5995
PubChem Compound439904
PDB IDNot Available
ChEBI ID16895
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. Gianotti AJ, Tower PA, Sheley JH, Conte PA, Spiro C, Ferro AJ, Fitchen JH, Riscoe MK: Selective killing of Klebsiella pneumoniae by 5-trifluoromethylthioribose. Chemotherapeutic exploitation of the enzyme 5-methylthioribose kinase. J Biol Chem. 1990 Jan 15;265(2):831-7. [PubMed:2153115 ]
  2. Della Ragione F, Carteni-Farina M, Gragnaniello V, Schettino MI, Zappia V: Purification and characterization of 5'-deoxy-5'-methylthioadenosine phosphorylase from human placenta. J Biol Chem. 1986 Sep 15;261(26):12324-9. [PubMed:3091600 ]
  3. Carteni-Farina M, della Ragione F, Cacciapuoti G, Porcelli M, Zappia V: Transport and metabolism of 5'-methylthioadenosine in human erythrocytes. Biochim Biophys Acta. 1983 Jan 19;727(2):221-9. [PubMed:6838867 ]
  4. Schroeder HR, Barnes CJ, Bohinski RC, Mallette MF: Biological production of 5-methylthioribose. Can J Microbiol. 1973 Nov;19(11):1347-54. [PubMed:4203512 ]