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Showing metabocard for 2-oxo-5-methylthiopentanoate (HMDB0304082)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:01:30 UTC
Update Date2021-09-24 07:01:30 UTC
HMDB IDHMDB0304082
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-oxo-5-methylthiopentanoate
Description2-oxo-5-methylthiopentanoate, also known as 5-(methylthio)-2-oxopentanoic-acid, is a member of the class of compounds known as thia fatty acids. Thia fatty acids are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain. 2-oxo-5-methylthiopentanoate is slightly soluble (in water) and a weakly acidic compound (based on its pKa). 2-oxo-5-methylthiopentanoate can be found in a number of food items such as wakame, soy bean, sea-buckthornberry, and oil palm, which makes 2-oxo-5-methylthiopentanoate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304082 (2-oxo-5-methylthiopentanoate)


  Mrv1652303082006202D          

 10  9  0  0  0  0            999 V2000
    1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    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  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  CHG  1   9  -1
M  END
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3D MOL for HMDB0304082 (2-oxo-5-methylthiopentanoate)

HMDB0304082
     RDKit          3D
2-oxo-5-methylthiopentanoate
 19 18  0  0  0  0  0  0  0  0999 V2000
    3.3224    0.1780   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5773   -0.4940    0.8704 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9927    0.3067    1.2593 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0161   -0.0537    0.1615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3447    0.5753    0.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2339    0.1808   -0.7018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1934    0.7599   -1.8322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1803   -0.8954   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2169   -1.4645    0.6217 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0410   -1.3142   -1.4781 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.7512    1.0711   -1.0059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2150   -0.6001   -1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3976    0.4216   -0.5137 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1023    1.3907    1.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6009   -0.1201    2.2060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0864   -1.1582    0.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3613    0.2900   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2794    1.6823    0.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7607    0.2077    1.3682 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  2  0
  6  8  1  0
  8  9  2  0
  8 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
  5 18  1  0
  5 19  1  0
M  CHG  1  10  -1
M  END
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3D SDF for HMDB0304082 (2-oxo-5-methylthiopentanoate)


  Mrv1652303082006202D          

 10  9  0  0  0  0            999 V2000
    1.0461    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605    1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3329    0.6039    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  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  CHG  1   9  -1
M  END
> <DATABASE_ID>
HMDB0304082

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O3S/c1-10-4-2-3-5(7)6(8)9/h2-4H2,1H3,(H,8,9)/p-1

> <INCHI_KEY>
MPJMAJLPWRBNBU-UHFFFAOYSA-M

> <FORMULA>
C6H9O3S

> <MOLECULAR_WEIGHT>
161.2

> <EXACT_MASS>
161.027788904

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.896227706680309

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-(methylsulfanyl)-2-oxopentanoate

> <ALOGPS_LOGP>
1.13

> <JCHEM_LOGP>
1.4126784546666666

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4371643752082464

> <JCHEM_PKA_STRONGEST_BASIC>
-9.657310759434493

> <JCHEM_POLAR_SURFACE_AREA>
57.199999999999996

> <JCHEM_REFRACTIVITY>
50.663000000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.21e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-methylthio-2-oxopentanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0304082 (2-oxo-5-methylthiopentanoate)

HMDB0304082
     RDKit          3D
2-oxo-5-methylthiopentanoate
 19 18  0  0  0  0  0  0  0  0999 V2000
    3.3224    0.1780   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5773   -0.4940    0.8704 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.9927    0.3067    1.2593 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0161   -0.0537    0.1615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3447    0.5753    0.4003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2339    0.1808   -0.7018 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1934    0.7599   -1.8322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1803   -0.8954   -0.4933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2169   -1.4645    0.6217 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0410   -1.3142   -1.4781 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.7512    1.0711   -1.0059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2150   -0.6001   -1.4217 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3976    0.4216   -0.5137 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1023    1.3907    1.4113 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6009   -0.1201    2.2060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0864   -1.1582    0.1828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3613    0.2900   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2794    1.6823    0.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7607    0.2077    1.3682 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  2  0
  6  8  1  0
  8  9  2  0
  8 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
  5 18  1  0
  5 19  1  0
M  CHG  1  10  -1
M  END
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PDB for HMDB0304082 (2-oxo-5-methylthiopentanoate)

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       1.953   2.667   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       3.286   3.437   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       9.955   1.127   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    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0304082 (2-oxo-5-methylthiopentanoate)

COMPND    HMDB0304082
HETATM    1  C1  UNL     1       3.322   0.178  -0.615  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.577  -0.494   0.870  1.00  0.00           S  
HETATM    3  C2  UNL     1       0.993   0.307   1.259  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.016  -0.054   0.161  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.345   0.575   0.400  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.234   0.181  -0.702  1.00  0.00           C  
HETATM    7  O1  UNL     1      -2.193   0.760  -1.832  1.00  0.00           O  
HETATM    8  C6  UNL     1      -3.180  -0.895  -0.493  1.00  0.00           C  
HETATM    9  O2  UNL     1      -3.217  -1.464   0.622  1.00  0.00           O  
HETATM   10  O3  UNL     1      -4.041  -1.314  -1.478  1.00  0.00           O1-
HETATM   11  H1  UNL     1       2.751   1.071  -1.006  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.215  -0.600  -1.422  1.00  0.00           H  
HETATM   13  H3  UNL     1       4.398   0.422  -0.514  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.102   1.391   1.411  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.601  -0.120   2.206  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.086  -1.158   0.183  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.361   0.290  -0.822  1.00  0.00           H  
HETATM   18  H8  UNL     1      -1.279   1.682   0.402  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.761   0.208   1.368  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   18   19
CONECT    6    7    7    8
CONECT    8    9    9   10
END
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SMILES for HMDB0304082 (2-oxo-5-methylthiopentanoate)

CSCCCC(=O)C([O-])=O
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INCHI for HMDB0304082 (2-oxo-5-methylthiopentanoate)

InChI=1S/C6H10O3S/c1-10-4-2-3-5(7)6(8)9/h2-4H2,1H3,(H,8,9)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-(5-Methylsulfanyl)oxopentanoateChEBI
2-(5-Methylsulfanyl)oxopentanoic acidGenerator
2-(5-Methylsulphanyl)oxopentanoateGenerator
2-(5-Methylsulphanyl)oxopentanoic acidGenerator
5-Methylthio-2-oxopentanoic acidGenerator
2-oxo-5-Methylthiopentanoic-acidMetaCyc
5-methylthio-2-OxopentanoateMetaCyc
2-oxo-5-Methylthiopentanoic acidGenerator
Chemical FormulaC6H9O3S
Average Molecular Weight161.2
Monoisotopic Molecular Weight161.027788904
IUPAC Name5-(methylsulfanyl)-2-oxopentanoate
Traditional Name5-methylthio-2-oxopentanoate
CAS Registry NumberNot Available
SMILES
CSCCCC(=O)C([O-])=O
InChI Identifier
InChI=1S/C6H10O3S/c1-10-4-2-3-5(7)6(8)9/h2-4H2,1H3,(H,8,9)/p-1
InChI KeyMPJMAJLPWRBNBU-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thia fatty acids. These are fatty acid derivatives obtained by insertion of a sulfur atom at specific positions in the chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentThia fatty acids
Alternative Parents
Substituents
  • Short-chain keto acid
  • Thia fatty acid
  • Alpha-keto acid
  • Keto acid
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Dialkylthioether
  • Thioether
  • Sulfenyl compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organosulfur compound
  • Organic oxygen compound
  • 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
logP1.13ALOGPS
logP1.41ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)3.44ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area57.2 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity50.66 m³·mol⁻¹ChemAxon
Polarizability15.9 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+134.95732859911
AllCCS[M+H-H2O]+131.05632859911
AllCCS[M+Na]+139.63432859911
AllCCS[M+NH4]+138.58832859911
AllCCS[M-H]-135.44932859911
AllCCS[M+Na-2H]-137.64832859911
AllCCS[M+HCOO]-140.11632859911
DeepCCS[M+H]+141.82430932474
DeepCCS[M-H]-138.68130932474
DeepCCS[M-2H]-175.80930932474
DeepCCS[M+Na]+150.50930932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-oxo-5-methylthiopentanoate,1TMS,isomer #1CSCCC=C(O[Si](C)(C)C)C(=O)[O-]1415.4Semi standard non polar33892256
2-oxo-5-methylthiopentanoate,1TMS,isomer #1CSCCC=C(O[Si](C)(C)C)C(=O)[O-]1467.9Standard non polar33892256
2-oxo-5-methylthiopentanoate,1TMS,isomer #1CSCCC=C(O[Si](C)(C)C)C(=O)[O-]1859.2Standard polar33892256
2-oxo-5-methylthiopentanoate,1TBDMS,isomer #1CSCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]1656.0Semi standard non polar33892256
2-oxo-5-methylthiopentanoate,1TBDMS,isomer #1CSCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]1677.0Standard non polar33892256
2-oxo-5-methylthiopentanoate,1TBDMS,isomer #1CSCCC=C(O[Si](C)(C)C(C)(C)C)C(=O)[O-]1973.2Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-5-methylthiopentanoate 10V, Negative-QTOFsplash10-03dj-5900000000-322a3253a0d98b20ea832019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-5-methylthiopentanoate 20V, Negative-QTOFsplash10-0002-9300000000-5d8397d09136d07600a52019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-oxo-5-methylthiopentanoate 40V, Negative-QTOFsplash10-0002-9000000000-9d1e3174cb9911789e7e2019-02-23Wishart 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 IDFDB030354
KNApSAcK IDNot Available
Chemspider ID24785626
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID58815
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