Showing metabocard for 5-Methylthioribose (MMDBc0029551)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-17 23:31:58 UTC
Update Date2022-08-31 13:43:12 UTC
Metabolite IDMMDBc0029551
Metabolite Identification
Common Name5-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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055d24adf9ab8>


  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
Download

3D MOL for #<Metabolite:0x000055d24adf9ab8>

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
Download

3D SDF for #<Metabolite:0x000055d24adf9ab8>


  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>
MMDBc0029551

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x000055d24adf9ab8>

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 #<Metabolite:0x000055d24adf9ab8>

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 #<Metabolite:0x000055d24adf9ab8>

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 #<Metabolite:0x000055d24adf9ab8>

CSC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O
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INCHI for #<Metabolite:0x000055d24adf9ab8>

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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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
Molecular FormulaC6H12O4S
Average Mass180.222
Monoisotopic Mass180.045629562
IUPAC Name(2R,3R,4S,5S)-5-[(methylsulfanyl)methyl]oxolane-2,3,4-triol
Traditional Name5-methylthio-D-ribose
CAS Registry Number23656-67-9
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