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Showing metabocard for 1,2-Dihydroxy-3-keto-5-methylthiopentene (HMDB0012134)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:19:47 UTC
Update Date2023-02-21 17:17:39 UTC
HMDB IDHMDB0012134
Secondary Accession Numbers
  • HMDB12134
Metabolite Identification
Common Name1,2-Dihydroxy-3-keto-5-methylthiopentene
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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

  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 HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

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 HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

  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>
HMDB0012134

> <DATABASE_NAME>
hmdb

> <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

$$$$
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3D-SDF for HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

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 HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

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 HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

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 HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

CSCCC(=O)C(\O)=C\O
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INCHI for HMDB0012134 (1,2-Dihydroxy-3-keto-5-methylthiopentene)

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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View in JSmolView NMR AssignmentsView Stereo Labels
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
Chemical FormulaC6H10O3S
Average Molecular Weight162.207
Monoisotopic Molecular Weight162.035064876
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 Number746507-19-7
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
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentAlpha-branched alpha,beta-unsaturated ketones
Alternative Parents
Substituents
  • Alpha-branched alpha,beta-unsaturated-ketone
  • Vinylogous acid
  • Enone
  • Alpha-hydroxy ketone
  • Acryloyl-group
  • Ketone
  • Enediol
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDFDB028796
KNApSAcK IDNot Available
Chemspider ID4575316
KEGG Compound IDC15606
BioCyc IDCPD-85
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5462190
PDB IDNot Available
ChEBI ID49252
Food Biomarker OntologyNot Available
VMH IDM00245
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. Enolase-phosphatase E1
General function:
Involved in catalytic activity
Specific function:
Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene).
Gene Name:
ENOPH1
Uniprot ID:
Q9UHY7
Molecular weight:
28932.44
Reactions
5-(Methylthio)-2,3-dioxopentyl phosphate + Water → 1,2-Dihydroxy-3-keto-5-methylthiopentene + Phosphatedetails
Enzyme Details
2. 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
General function:
Involved in metal ion binding
Specific function:
Catalyzes the formation of formate and 2-keto-4-methylthiobutyrate (KMTB) from 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene). Also down-regulates cell migration mediated by MMP14. Necessary for hepatitis C virus replication in an otherwise non-permissive cell line.
Gene Name:
ADI1
Uniprot ID:
Q9BV57
Molecular weight:
21498.23
Reactions
1,2-Dihydroxy-3-keto-5-methylthiopentene + Oxygen → 2-Oxo-4-methylthiobutanoic acid + Formic aciddetails
1,2-Dihydroxy-3-keto-5-methylthiopentene + Oxygen → 3-Methylthiopropionic acid + Formic acid + Carbon monoxidedetails