Hmdb loader

Showing metabocard for 2-oxo-6-methylthiohexanoate (HMDB0304083)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:02:02 UTC
Update Date2021-09-24 07:02:02 UTC
HMDB IDHMDB0304083
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-oxo-6-methylthiohexanoate
Description2-oxo-6-methylthiohexanoate, also known as 6-(methylthio)-2-oxohexanoic acid, belongs to medium-chain keto acids and derivatives class of compounds. Those are keto acids with a 6 to 12 carbon atoms long side chain. 2-oxo-6-methylthiohexanoate is practically insoluble (in water) and a weakly acidic compound (based on its pKa). 2-oxo-6-methylthiohexanoate can be found in a number of food items such as soursop, nance, turmeric, and strawberry guava, which makes 2-oxo-6-methylthiohexanoate a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304083 (2-oxo-6-methylthiohexanoate)


  Mrv1533005141521382D          

 11 10  0  0  0  0            999 V2000
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  CHG  1  10  -1
M  END
Download

3D MOL for HMDB0304083 (2-oxo-6-methylthiohexanoate)

HMDB0304083
     RDKit          3D
2-oxo-6-methylthiohexanoate
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.8028    0.3553    1.0304 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1728   -1.3344    0.8503 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7380   -1.2695   -0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6191   -0.5041    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6054   -0.4206   -0.4510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6562    0.3617    0.3226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8971    0.4865   -0.4811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9372   -0.0319   -1.6539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0243    1.1869    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9504    1.6776    1.2160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1926    1.3209   -0.6384 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.2141    1.0904    0.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8618    0.3430    0.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7880    0.6548    2.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3463   -2.3167   -0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9804   -0.8627   -1.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9668    0.5159    0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3220   -0.9979    1.3740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4026    0.0496   -1.4289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0238   -1.4474   -0.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8705   -0.2307    1.2401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2521    1.3736    0.5484 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
  7  8  2  0
  7  9  1  0
  9 10  2  0
  9 11  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  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
M  CHG  1  11  -1
M  END
Download

3D SDF for HMDB0304083 (2-oxo-6-methylthiohexanoate)


  Mrv1533005141521382D          

 11 10  0  0  0  0            999 V2000
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  CHG  1  10  -1
M  END
> <DATABASE_ID>
HMDB0304083

> <DATABASE_NAME>
hmdb

> <SMILES>
CSCCCCC(=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O3S/c1-11-5-3-2-4-6(8)7(9)10/h2-5H2,1H3,(H,9,10)/p-1

> <INCHI_KEY>
GRUGZHAOXOPASC-UHFFFAOYSA-M

> <FORMULA>
C7H11O3S

> <MOLECULAR_WEIGHT>
175.22

> <EXACT_MASS>
175.043438968

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
17.975545619450617

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-(methylsulfanyl)-2-oxohexanoate

> <ALOGPS_LOGP>
1.39

> <JCHEM_LOGP>
1.857247119666667

> <ALOGPS_LOGS>
-2.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.54411123557643

> <JCHEM_PKA_STRONGEST_BASIC>
-9.656719958293701

> <JCHEM_POLAR_SURFACE_AREA>
57.199999999999996

> <JCHEM_REFRACTIVITY>
55.264

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.50e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-(methylsulfanyl)-2-oxohexanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304083 (2-oxo-6-methylthiohexanoate)

HMDB0304083
     RDKit          3D
2-oxo-6-methylthiohexanoate
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.8028    0.3553    1.0304 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1728   -1.3344    0.8503 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.7380   -1.2695   -0.2467 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6191   -0.5041    0.4263 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6054   -0.4206   -0.4510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6562    0.3617    0.3226 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8971    0.4865   -0.4811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9372   -0.0319   -1.6539 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0243    1.1869    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9504    1.6776    1.2160 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1926    1.3209   -0.6384 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.2141    1.0904    0.4558 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8618    0.3430    0.6678 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7880    0.6548    2.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3463   -2.3167   -0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9804   -0.8627   -1.2394 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9668    0.5159    0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3220   -0.9979    1.3740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4026    0.0496   -1.4289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0238   -1.4474   -0.5703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8705   -0.2307    1.2401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2521    1.3736    0.5484 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
  7  8  2  0
  7  9  1  0
  9 10  2  0
  9 11  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  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  0
  6 22  1  0
M  CHG  1  11  -1
M  END
Download

PDB for HMDB0304083 (2-oxo-6-methylthiohexanoate)

HEADER    PROTEIN                                 14-MAY-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   14-MAY-15         0                                  
HETATM    1  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       6.930   4.001   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
Download

3D PDB for HMDB0304083 (2-oxo-6-methylthiohexanoate)

COMPND    HMDB0304083
HETATM    1  C1  UNL     1       3.803   0.355   1.030  1.00  0.00           C  
HETATM    2  S1  UNL     1       3.173  -1.334   0.850  1.00  0.00           S  
HETATM    3  C2  UNL     1       1.738  -1.270  -0.247  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.619  -0.504   0.426  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.605  -0.421  -0.451  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.656   0.362   0.323  1.00  0.00           C  
HETATM    7  C6  UNL     1      -2.897   0.486  -0.481  1.00  0.00           C  
HETATM    8  O1  UNL     1      -2.937  -0.032  -1.654  1.00  0.00           O  
HETATM    9  C7  UNL     1      -4.024   1.187   0.078  1.00  0.00           C  
HETATM   10  O2  UNL     1      -3.950   1.678   1.216  1.00  0.00           O  
HETATM   11  O3  UNL     1      -5.193   1.321  -0.638  1.00  0.00           O1-
HETATM   12  H1  UNL     1       3.214   1.090   0.456  1.00  0.00           H  
HETATM   13  H2  UNL     1       4.862   0.343   0.668  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.788   0.655   2.090  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.346  -2.317  -0.378  1.00  0.00           H  
HETATM   16  H5  UNL     1       1.980  -0.863  -1.239  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.967   0.516   0.660  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.322  -0.998   1.374  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.403   0.050  -1.429  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.024  -1.447  -0.570  1.00  0.00           H  
HETATM   21  H10 UNL     1      -1.870  -0.231   1.240  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.252   1.374   0.548  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7   21   22
CONECT    7    8    8    9
CONECT    9   10   10   11
END
Download

SMILES for HMDB0304083 (2-oxo-6-methylthiohexanoate)

CSCCCCC(=O)C([O-])=O
Download

INCHI for HMDB0304083 (2-oxo-6-methylthiohexanoate)

InChI=1S/C7H12O3S/c1-11-5-3-2-4-6(8)7(9)10/h2-5H2,1H3,(H,9,10)/p-1
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
6-(Methylsulfanyl)-2-oxohexanoic acidGenerator
6-(Methylsulphanyl)-2-oxohexanoateGenerator
6-(Methylsulphanyl)-2-oxohexanoic acidGenerator
2-oxo-6-Methylthiohexanoic acidMetaCyc, Generator
Chemical FormulaC7H11O3S
Average Molecular Weight175.22
Monoisotopic Molecular Weight175.043438968
IUPAC Name6-(methylsulfanyl)-2-oxohexanoate
Traditional Name6-(methylsulfanyl)-2-oxohexanoate
CAS Registry NumberNot Available
SMILES
CSCCCCC(=O)C([O-])=O
InChI Identifier
InChI=1S/C7H12O3S/c1-11-5-3-2-4-6(8)7(9)10/h2-5H2,1H3,(H,9,10)/p-1
InChI KeyGRUGZHAOXOPASC-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as medium-chain keto acids and derivatives. These are keto acids with a 6 to 12 carbon atoms long side chain.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassMedium-chain keto acids and derivatives
Direct ParentMedium-chain keto acids and derivatives
Alternative Parents
Substituents
  • Medium-chain keto acid
  • Thia fatty acid
  • Alpha-keto acid
  • Fatty acyl
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Carbonyl group
  • Organooxygen compound
  • Organosulfur compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP1.39ALOGPS
logP1.86ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)3.54ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area57.2 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity55.26 m³·mol⁻¹ChemAxon
Polarizability17.98 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+138.3432859911
AllCCS[M+H-H2O]+134.53832859911
AllCCS[M+Na]+142.89832859911
AllCCS[M+NH4]+141.87832859911
AllCCS[M-H]-139.65332859911
AllCCS[M+Na-2H]-141.49332859911
AllCCS[M+HCOO]-143.57932859911
DeepCCS[M+H]+145.22130932474
DeepCCS[M-H]-141.92830932474
DeepCCS[M-2H]-179.15630932474
DeepCCS[M+Na]+153.99630932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-oxo-6-methylthiohexanoate,1TMS,isomer #1CSCCCC=C(O[Si](C)(C)C)C(=O)[O-]1520.4Semi standard non polar33892256
2-oxo-6-methylthiohexanoate,1TMS,isomer #1CSCCCC=C(O[Si](C)(C)C)C(=O)[O-]1560.2Standard non polar33892256
2-oxo-6-methylthiohexanoate,1TMS,isomer #1CSCCCC=C(O[Si](C)(C)C)C(=O)[O-]1937.8Standard polar33892256
2-oxo-6-methylthiohexanoate,1TBDMS,isomer #1CSCCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]1760.0Semi standard non polar33892256
2-oxo-6-methylthiohexanoate,1TBDMS,isomer #1CSCCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]1767.8Standard non polar33892256
2-oxo-6-methylthiohexanoate,1TBDMS,isomer #1CSCCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]2045.7Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-6-methylthiohexanoate 10V, Negative-QTOFsplash10-004j-4900000000-508cdcde3e6d2c2bfea92019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-6-methylthiohexanoate 20V, Negative-QTOFsplash10-0002-9300000000-3327e6a97a46a5439c5f2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-6-methylthiohexanoate 40V, Negative-QTOFsplash10-0002-9000000000-00c2a45e3b133b2856cd2019-02-23Wishart LabView Spectrum
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 IDFDB030355
KNApSAcK IDNot Available
Chemspider ID24784858
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44237195
PDB IDNot Available
ChEBI IDNot Available
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 ReferencesNot Available