5-Methylthioribose (ECMDB01087) (M2MDB000249)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)Transporters (4)XML
Proteins (341)
Record Information
Version2.0
Creation Date2012-05-31 13:44:57 -0600
Update Date2015-06-03 15:53:43 -0600
Secondary Accession Numbers
  • ECMDB01087
Identification
Name:5-Methylthioribose
DescriptionS-methyl-5-thio-D-ribose is a product of the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. This enzyme catalyzes the irreversible cleavage of the glycosidic bond in 5'-methylthioadenosine (MTA) to produce adenine and the corresponding thioribose, 5'-methylthioribose.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5-Deoxy-5-(methylthio)ribose
  • 5-Methylthio-D-ribose
  • 5-Methylthioribose
  • S-methyl-5-thio-D-ribofuranose
  • MTR
  • S(5)-Methyl-5-thio-D-ribose
  • S-Methyl-5-thio-D-ribofuranose
  • S5-Methyl-5-thio-D-ribose
Chemical Formula:C6H12O4S
Weight:Average: 180.222
Monoisotopic: 180.045629562
InChI Key:OLVVOVIFTBSBBH-KVTDHHQDSA-N
InChI: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
CAS number:23656-67-9
IUPAC Name:(2R,3R,4S,5S)-5-[(methylsulfanyl)methyl]oxolane-2,3,4-triol
Traditional IUPAC Name:5-methylthio-D-ribose
SMILES:CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
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
Physical Properties
State:Solid
Charge:0
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility176 g/LALOGPS
logP-1.4ALOGPS
logP-0.82ChemAxon
logS-0.01ALOGPS
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
5'-Methylthioadenosine + Water > 5-Methylthioribose + Adenine
5'-Methylthioadenosine + Water <> Adenine + 5-Methylthioribose
5'-S-methyl-5'-thioadenosine + Water > 5-Methylthioribose + Adenine
SMPDB Pathways:
S-adenosyl-L-methionine biosynthesisPW000837 ThumbThumb?image type=greyscaleThumb?image type=simple
Spermidine biosynthesis and metabolismPW002085 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Cysteine and methionine metabolism ec00270
EcoCyc Pathways:
  • S-methyl-5'-thioadenosine degradation IV PWY0-1391
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0nor-9600000000-757c4b3ed6add1bdc168View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0719-9247000000-321d54ddf2f38682b57cView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0900000000-7914d8991b0a6af1d99fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-02ai-2900000000-e36191d55523024bf643View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0bvj-9500000000-94cbb1e527c7c7e21314View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-9200000000-21073f76322842d53a46View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-9300000000-89d811f24fdb17e739e8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0002-9000000000-ed328bd35b3fe1440450View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-1900000000-aefd2630eb3d70da8200View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0002-9100000000-57ad8e0e93b83006dc3cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0002-9000000000-789718691297aaebb3adView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01qa-4900000000-1a70ce18540d6a0916d8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-8900000000-ca12a9fcff10da622383View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03dj-9000000000-e18a37fac06996f6a660View in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
  • 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
  • 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
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16895
HMDB IDHMDB01087
Pubchem Compound ID494
Kegg IDC03089
ChemSpider ID388938
Wikipedia IDNot Available
BioCyc IDCPD-560
EcoCyc IDCPD-560

Enzymes

Protein Details
1. 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
General function:
Involved in adenosylhomocysteine nucleosidase activity
Specific function:
Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Can also use 5'-isobutylthioadenosine, 5'-n- butylthioadenosine, S-adenosyl-D-homocysteine, decarboxylated adenosylhomocysteine, deaminated adenosylhomocysteine and S-2-aza- adenosylhomocysteine as substrates
Gene Name:
mtnN
Uniprot ID:
P0AF12
Molecular weight:
24354
Reactions
S-adenosyl-L-homocysteine + H(2)O = S-(5-deoxy-D-ribos-5-yl)-L-homocysteine + adenine.
S-methyl-5'-thioadenosine + H(2)O = S-methyl-5-thio-D-ribose + adenine.

Transporters

Protein Details
1. Outer membrane protein N
General function:
Involved in transporter activity
Specific function:
Non-specific porin
Gene Name:
ompN
Uniprot ID:
P77747
Molecular weight:
41220
Protein Details
2. Outer membrane pore protein E
General function:
Involved in transporter activity
Specific function:
Uptake of inorganic phosphate, phosphorylated compounds, and some other negatively charged solutes
Gene Name:
phoE
Uniprot ID:
P02932
Molecular weight:
38922
Protein Details
3. Outer membrane protein F
General function:
Involved in transporter activity
Specific function:
OmpF is a porin that forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane. It is also a receptor for the bacteriophage T2
Gene Name:
ompF
Uniprot ID:
P02931
Molecular weight:
39333
Protein Details
4. Outer membrane protein C
General function:
Involved in transporter activity
Specific function:
Forms passive diffusion pores which allow small molecular weight hydrophilic materials across the outer membrane
Gene Name:
ompC
Uniprot ID:
P06996
Molecular weight:
40368