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Showing metabocard for 5-Methylthioribose (HMDB0001087)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:26 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?1676999726
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001087 (5-Methylthioribose)


  Mrv1652309042000182D          

 11 11  0  0  0  0            999 V2000
10000.682810000.8689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.397610000.4570    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
10002.110310000.8689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.1760 9999.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.849610000.7103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3877 9999.0186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.298910000.9508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.631510000.4658    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.8864 9999.6812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.7114 9999.6812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.966310000.4658    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
 11  1  1  6  0  0  0
 10  4  1  1  0  0  0
  9  6  1  1  0  0  0
  8  5  1  6  0  0  0
M  END
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3D MOL for HMDB0001087 (5-Methylthioribose)

HMDB0001087
     RDKit          3D
5-Methylthioribose
 23 23  0  0  0  0  0  0  0  0999 V2000
    3.5053    0.6661    0.2555 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7881   -0.0653   -1.2392 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3452   -1.0614   -0.8047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2183   -0.2199   -0.2672 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2226    0.7323   -1.1752 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3191    1.2737   -0.4660 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1021    2.0884   -1.2416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0852    0.0478    0.0341 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6115    0.2368    1.2894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0347   -1.0246   -0.0248 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9620   -1.7657    1.1498 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -0.0505    0.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9506    1.6579    0.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6959    0.7852    0.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9879   -1.6625   -1.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6380   -1.7589    0.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4776    0.2849    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9112    1.7814    0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4866    2.8279   -0.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9123   -0.1098   -0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3260   -0.4589    1.9452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2854   -1.6949   -0.8644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5911   -2.5099    1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  1
  6 18  1  1
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  6
 11 23  1  0
M  END
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3D SDF for HMDB0001087 (5-Methylthioribose)


  Mrv1652309042000182D          

 11 11  0  0  0  0            999 V2000
10000.682810000.8689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.397610000.4570    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
10002.110310000.8689    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.1760 9999.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.849610000.7103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.3877 9999.0186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.298910000.9508    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.631510000.4658    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9998.8864 9999.6812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.7114 9999.6812    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9999.966310000.4658    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7  8  1  0  0  0  0
  7 11  1  0  0  0  0
 11  1  1  6  0  0  0
 10  4  1  1  0  0  0
  9  6  1  1  0  0  0
  8  5  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0001087

> <DATABASE_NAME>
hmdb

> <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_KEY>
OLVVOVIFTBSBBH-KVTDHHQDSA-N

> <FORMULA>
C6H12O4S

> <MOLECULAR_WEIGHT>
180.222

> <EXACT_MASS>
180.045629562

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.66958268765486

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S)-5-[(methylsulfanyl)methyl]oxolane-2,3,4-triol

> <ALOGPS_LOGP>
-1.39

> <JCHEM_LOGP>
-0.8197331299999999

> <ALOGPS_LOGS>
-0.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.935026951592619

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.30859254818828

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6587382890277365

> <JCHEM_POLAR_SURFACE_AREA>
69.92

> <JCHEM_REFRACTIVITY>
40.79449999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.76e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylthio-D-ribose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001087 (5-Methylthioribose)

HMDB0001087
     RDKit          3D
5-Methylthioribose
 23 23  0  0  0  0  0  0  0  0999 V2000
    3.5053    0.6661    0.2555 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7881   -0.0653   -1.2392 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3452   -1.0614   -0.8047 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2183   -0.2199   -0.2672 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2226    0.7323   -1.1752 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3191    1.2737   -0.4660 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1021    2.0884   -1.2416 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0852    0.0478    0.0341 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6115    0.2368    1.2894 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0347   -1.0246   -0.0248 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9620   -1.7657    1.1498 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -0.0505    0.6630 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9506    1.6579    0.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6959    0.7852    0.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9879   -1.6625   -1.6479 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6380   -1.7589    0.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4776    0.2849    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9112    1.7814    0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4866    2.8279   -0.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9123   -0.1098   -0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3260   -0.4589    1.9452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2854   -1.6949   -0.8644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5911   -2.5099    1.1490 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 10  4  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  1
  6 18  1  1
  7 19  1  0
  8 20  1  6
  9 21  1  0
 10 22  1  6
 11 23  1  0
M  END
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PDB for HMDB0001087 (5-Methylthioribose)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.9418668.289   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0    8669.2768667.520   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0    8670.6068668.289   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8666.9958664.819   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0    8662.6538667.993   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8663.6578664.835   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8665.3588668.441   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    8664.1128667.536   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8664.5888666.072   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8666.1288666.072   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8666.6048667.536   0.000  0.00  0.00           C+0
CONECT    1    2   11                                                       
CONECT    2    1    3                                                       
CONECT    3    2                                                            
CONECT    4   10                                                            
CONECT    5    8                                                            
CONECT    6    9                                                            
CONECT    7    8   11                                                       
CONECT    8    9    7    5                                                  
CONECT    9    8   10    6                                                  
CONECT   10    9   11    4                                                  
CONECT   11   10    7    1                                                  
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for HMDB0001087 (5-Methylthioribose)

COMPND    HMDB0001087
HETATM    1  C1  UNL     1       3.505   0.666   0.256  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.788  -0.065  -1.239  1.00  0.00           S  
HETATM    3  C2  UNL     1       1.345  -1.061  -0.805  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.218  -0.220  -0.267  1.00  0.00           C  
HETATM    5  O1  UNL     1      -0.223   0.732  -1.175  1.00  0.00           O  
HETATM    6  C4  UNL     1      -1.319   1.274  -0.466  1.00  0.00           C  
HETATM    7  O2  UNL     1      -2.102   2.088  -1.242  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.085   0.048   0.034  1.00  0.00           C  
HETATM    9  O3  UNL     1      -2.612   0.237   1.289  1.00  0.00           O  
HETATM   10  C6  UNL     1      -1.035  -1.025  -0.025  1.00  0.00           C  
HETATM   11  O4  UNL     1      -0.962  -1.766   1.150  1.00  0.00           O  
HETATM   12  H1  UNL     1       4.243  -0.051   0.663  1.00  0.00           H  
HETATM   13  H2  UNL     1       3.951   1.658   0.058  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.696   0.785   0.981  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.988  -1.663  -1.648  1.00  0.00           H  
HETATM   16  H5  UNL     1       1.638  -1.759   0.023  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.478   0.285   0.677  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.911   1.781   0.433  1.00  0.00           H  
HETATM   19  H8  UNL     1      -2.487   2.828  -0.682  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.912  -0.110  -0.684  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.326  -0.459   1.945  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.285  -1.695  -0.864  1.00  0.00           H  
HETATM   23  H12 UNL     1      -1.591  -2.510   1.149  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3
CONECT    3    4   15   16
CONECT    4    5   10   17
CONECT    5    6
CONECT    6    7    8   18
CONECT    7   19
CONECT    8    9   10   20
CONECT    9   21
CONECT   10   11   22
CONECT   11   23
END
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SMILES for HMDB0001087 (5-Methylthioribose)

CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
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INCHI for HMDB0001087 (5-Methylthioribose)

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
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View in JSmolView NMR AssignmentsView Stereo Labels
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
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
RoleNot 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 PropertiesNot Available
Predicted Molecular 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
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
DeepCCS[M-H]-138.59330932474
DeepCCS[M-2H]-172.34730932474
DeepCCS[M+Na]+147.51130932474
AllCCS[M+H]+140.032859911
AllCCS[M+H-H2O]+135.932859911
AllCCS[M+NH4]+143.932859911
AllCCS[M+Na]+145.032859911
AllCCS[M-H]-137.832859911
AllCCS[M+Na-2H]-139.332859911
AllCCS[M+HCOO]-141.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.21 minutes32390414
Predicted by Siyang on May 30, 202210.3748 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.46 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid175.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1060.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid335.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid49.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid188.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid62.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid263.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid309.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)426.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid695.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid133.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid855.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid203.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid187.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate542.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA355.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water145.7 seconds40023050

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

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
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 ]