Showing metabocard for 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one (MMDBc0054135)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-06-05 22:54:43 UTC
Update Date2022-09-01 02:27:29 UTC
Metabolite IDMMDBc0054135
Metabolite Identification
Common Name1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Description1,2-Dihydroxy-3-keto-5-methylthiopentene, also known as 1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one, belongs to the class of organic compounds known as alpha-branched alpha,beta-unsaturated ketones. These are alpha,beta-unsaturated ketones that carry a branch on the alpha carbon. They have the generic structure RC(=O)C(R')=C, R = organyl group and R'= any heteroatom. 1,2-Dihydroxy-3-keto-5-methylthiopentene exists in all living species, ranging from bacteria to plants to humans. 1,2-Dihydroxy-3-keto-5-methylthiopentene has been detected, but not quantified in, several different foods, such as oats (Avena sativa), endives (Cichorium endivia), lambsquarters (Chenopodium album), capers (Capparis spinosa), and babassu palms (Attalea speciosa). This could make 1,2-dihydroxy-3-keto-5-methylthiopentene a potential biomarker for the consumption of these foods. 1,2-Dihydroxy-3-keto-5-methylthiopentene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a small amount of articles have been published on 1,2-Dihydroxy-3-keto-5-methylthiopentene.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007fecb40aabd8>


  Mrv1652309042000342D          

 10  9  0  0  0  0            999 V2000
   14.1458  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9945  -11.7315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7117  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8542  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2885  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713  -11.7315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1371  -11.7315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2885  -12.9669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713  -10.9039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4287  -11.7315    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3 10  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  6  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007fecb40aabd8>

HMDB0012134
     RDKit          3D
1,2-Dihydroxy-3-keto-5-methylthiopentene
 20 19  0  0  0  0  0  0  0  0999 V2000
    3.3243   -0.1668    0.4443 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099    0.8904   -0.9079 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0341    1.1779   -0.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2737   -0.1186   -1.2595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1817    0.1756   -1.2817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6054    0.7736   -2.3060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885   -0.1795   -0.2262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4416    0.1398   -0.3375 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7396   -0.8065    0.8845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6966   -1.1171    1.8706 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4469   -0.1112    0.4979 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1011   -1.2484    0.2780 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9588    0.1714    1.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8418    1.8855   -1.7956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6434    1.6671   -0.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905   -0.3780   -2.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5837   -0.8643   -0.5343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1931   -0.4897   -0.1918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7003   -1.0781    1.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9615   -0.3232    2.4522 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  2  0
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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3D SDF for #<Metabolite:0x00007fecb40aabd8>


  Mrv1652309042000342D          

 10  9  0  0  0  0            999 V2000
   14.1458  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9945  -11.7315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7117  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8542  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2885  -12.1394    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713  -11.7315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1371  -11.7315    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2885  -12.9669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5713  -10.9039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4287  -11.7315    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  2  5  1  0  0  0  0
  3 10  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  8  2  0  0  0  0
  5  6  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054135

> <DATABASE_NAME>
MIME

> <SMILES>
CSCCC(=O)C(\O)=C\O

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O3S/c1-10-3-2-5(8)6(9)4-7/h4,7,9H,2-3H2,1H3/b6-4-

> <INCHI_KEY>
CILXJJLQPTUUSS-XQRVVYSFSA-N

> <FORMULA>
C6H10O3S

> <MOLECULAR_WEIGHT>
162.207

> <EXACT_MASS>
162.035064876

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
16.294051900205332

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1Z)-1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
0.8116459593333338

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.558186339804077

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.30665894402364

> <JCHEM_PKA_STRONGEST_BASIC>
-3.967606300887529

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
41.8688

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1Z)-1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007fecb40aabd8>

HMDB0012134
     RDKit          3D
1,2-Dihydroxy-3-keto-5-methylthiopentene
 20 19  0  0  0  0  0  0  0  0999 V2000
    3.3243   -0.1668    0.4443 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8099    0.8904   -0.9079 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.0341    1.1779   -0.9499 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2737   -0.1186   -1.2595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1817    0.1756   -1.2817 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6054    0.7736   -2.3060 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0885   -0.1795   -0.2262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4416    0.1398   -0.3375 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7396   -0.8065    0.8845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6966   -1.1171    1.8706 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4469   -0.1112    0.4979 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1011   -1.2484    0.2780 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9588    0.1714    1.4346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8418    1.8855   -1.7956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6434    1.6671   -0.0455 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905   -0.3780   -2.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5837   -0.8643   -0.5343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1931   -0.4897   -0.1918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7003   -1.0781    1.0232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9615   -0.3232    2.4522 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  2  0
  5  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  4 17  1  0
  8 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007fecb40aabd8>

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      26.405 -22.660   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      22.390 -21.899   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      23.729 -22.660   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.395 -22.660   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      21.072 -22.660   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.733 -21.899   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      17.056 -21.899   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      21.072 -24.205   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      19.733 -20.354   0.000  0.00  0.00           O+0
HETATM   10  S   UNK     0      25.067 -21.899   0.000  0.00  0.00           S+0
CONECT    1   10                                                            
CONECT    2    3    5                                                       
CONECT    3    2   10                                                       
CONECT    4    6    7                                                       
CONECT    5    2    8    6                                                  
CONECT    6    4    5    9                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    1    3                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007fecb40aabd8>

COMPND    HMDB0012134
HETATM    1  C1  UNL     1       3.324  -0.167   0.444  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.810   0.890  -0.908  1.00  0.00           S  
HETATM    3  C2  UNL     1       1.034   1.178  -0.950  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.274  -0.119  -1.260  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.182   0.176  -1.282  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.605   0.774  -2.306  1.00  0.00           O  
HETATM    7  C5  UNL     1      -2.088  -0.179  -0.226  1.00  0.00           C  
HETATM    8  O2  UNL     1      -3.442   0.140  -0.338  1.00  0.00           O  
HETATM    9  C6  UNL     1      -1.740  -0.807   0.885  1.00  0.00           C  
HETATM   10  O3  UNL     1      -2.697  -1.117   1.871  1.00  0.00           O  
HETATM   11  H1  UNL     1       4.447  -0.111   0.498  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.101  -1.248   0.278  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.959   0.171   1.435  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.842   1.886  -1.796  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.643   1.667  -0.046  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.591  -0.378  -2.309  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.584  -0.864  -0.534  1.00  0.00           H  
HETATM   18  H8  UNL     1      -4.193  -0.490  -0.192  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.700  -1.078   1.023  1.00  0.00           H  
HETATM   20  H10 UNL     1      -2.962  -0.323   2.452  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3
CONECT    3    4   14   15
CONECT    4    5   16   17
CONECT    5    6    6    7
CONECT    7    8    9    9
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007fecb40aabd8>

CSCCC(=O)C(\O)=C\O
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INCHI for #<Metabolite:0x00007fecb40aabd8>

InChI=1S/C6H10O3S/c1-10-3-2-5(8)6(9)4-7/h4,7,9H,2-3H2,1H3/b6-4-
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Synonyms
ValueSource
1,2-Dihydroxy-5-(methylsulfanyl)pent-1-en-3-oneChEBI
1,2-Dihydroxy-5-(methylsulphanyl)pent-1-en-3-oneGenerator
AcireductoneChEBI, HMDB
1,2-Dihydroxy-3-keto-5-methylthiopentaneHMDB
1,2-Dihydroxy-3-keto-5-methylthiopentene anionHMDB
1,2-Dihydroxy-5-(methylthio)pent-1-en-3-oneHMDB
Molecular FormulaC6H10O3S
Average Mass162.207
Monoisotopic Mass162.035064876
IUPAC Name(1Z)-1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
Traditional Name(1Z)-1,2-dihydroxy-5-(methylsulfanyl)pent-1-en-3-one
CAS Registry NumberNot Available
SMILES
CSCCC(=O)C(\O)=C\O
InChI Identifier
InChI=1S/C6H10O3S/c1-10-3-2-5(8)6(9)4-7/h4,7,9H,2-3H2,1H3/b6-4-
InChI KeyCILXJJLQPTUUSS-XQRVVYSFSA-N