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Showing metabocard for 3-S-methylmercaptopropionate (HMDB0304155)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 07:37:51 UTC
Update Date2021-09-24 07:37:51 UTC
HMDB IDHMDB0304155
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-S-methylmercaptopropionate
Description3-s-methylmercaptopropionate, also known as 3-methylthiopropionic acid or 3-(methylsulfanyl)propanoic acid, is a member of the class of compounds known as straight chain fatty acids. Straight chain fatty acids are fatty acids with a straight aliphatic chain. 3-s-methylmercaptopropionate is soluble (in water) and a weakly acidic compound (based on its pKa). 3-s-methylmercaptopropionate can be found in a number of food items such as other bread, italian sweet red pepper, triticale, and pot marjoram, which makes 3-s-methylmercaptopropionate a potential biomarker for the consumption of these food products.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304155 (3-S-methylmercaptopropionate)


  Mrv1533007131514092D          

  7  6  0  0  0  0            999 V2000
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
M  CHG  1   6  -1
M  END
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3D MOL for HMDB0304155 (3-S-methylmercaptopropionate)

HMDB0304155
     RDKit          3D
3-S-methylmercaptopropionate
 14 13  0  0  0  0  0  0  0  0999 V2000
   -2.4071    0.0100    0.2166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4206    0.4849   -1.2399 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    0.7747   -0.6466 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8820   -0.5266   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2636   -0.3121    0.3256 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8162    0.8374    0.3098 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0497   -1.3377    0.8294 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.9879    0.4515    1.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4699    0.2214    0.0907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -1.1053    0.2881 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460    1.1558   -1.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833    1.5092    0.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8966   -1.2758   -0.9641 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2727   -0.8875    0.6841 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
M  CHG  1   7  -1
M  END
Download

3D SDF for HMDB0304155 (3-S-methylmercaptopropionate)


  Mrv1533007131514092D          

  7  6  0  0  0  0            999 V2000
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539   -0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  4  2  0  0  0  0
  6  4  1  0  0  0  0
  7  1  1  0  0  0  0
  7  3  1  0  0  0  0
M  CHG  1   6  -1
M  END
> <DATABASE_ID>
HMDB0304155

> <DATABASE_NAME>
hmdb

> <SMILES>
CSCCC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O2S/c1-7-3-2-4(5)6/h2-3H2,1H3,(H,5,6)/p-1

> <INCHI_KEY>
CAOMCZAIALVUPA-UHFFFAOYSA-M

> <FORMULA>
C4H7O2S

> <MOLECULAR_WEIGHT>
119.16

> <EXACT_MASS>
119.017224219

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
11.803417161346623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(methylsulfanyl)propanoate

> <ALOGPS_LOGP>
0.37

> <JCHEM_LOGP>
0.8347975820000002

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.676434451839513

> <JCHEM_POLAR_SURFACE_AREA>
40.129999999999995

> <JCHEM_REFRACTIVITY>
40.562000000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.68e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methylthiopropionate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0304155 (3-S-methylmercaptopropionate)

HMDB0304155
     RDKit          3D
3-S-methylmercaptopropionate
 14 13  0  0  0  0  0  0  0  0999 V2000
   -2.4071    0.0100    0.2166 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4206    0.4849   -1.2399 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.2820    0.7747   -0.6466 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8820   -0.5266   -0.1611 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2636   -0.3121    0.3256 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8162    0.8374    0.3098 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0497   -1.3377    0.8294 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.9879    0.4515    1.1379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4699    0.2214    0.0907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3064   -1.1053    0.2881 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8460    1.1558   -1.5268 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2833    1.5092    0.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8966   -1.2758   -0.9641 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2727   -0.8875    0.6841 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
M  CHG  1   7  -1
M  END
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PDB for HMDB0304155 (3-S-methylmercaptopropionate)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0      -1.127   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.207  -0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O-1
HETATM    7  S   UNK     0       0.206   0.770   0.000  0.00  0.00           S+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    7                                                       
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4                                                            
CONECT    7    1    3                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0304155 (3-S-methylmercaptopropionate)

COMPND    HMDB0304155
HETATM    1  C1  UNL     1      -2.407   0.010   0.217  1.00  0.00           C  
HETATM    2  S1  UNL     1      -1.421   0.485  -1.240  1.00  0.00           S  
HETATM    3  C2  UNL     1       0.282   0.775  -0.647  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.882  -0.527  -0.161  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.264  -0.312   0.326  1.00  0.00           C  
HETATM    6  O1  UNL     1       2.816   0.837   0.310  1.00  0.00           O  
HETATM    7  O2  UNL     1       3.050  -1.338   0.829  1.00  0.00           O1-
HETATM    8  H1  UNL     1      -1.988   0.452   1.138  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.470   0.221   0.091  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.306  -1.105   0.288  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.846   1.156  -1.527  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.283   1.509   0.193  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.897  -1.276  -0.964  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.273  -0.888   0.684  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6    6    7
END
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SMILES for HMDB0304155 (3-S-methylmercaptopropionate)

CSCCC([O-])=O
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INCHI for HMDB0304155 (3-S-methylmercaptopropionate)

InChI=1S/C4H8O2S/c1-7-3-2-4(5)6/h2-3H2,1H3,(H,5,6)/p-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-(Methylsulfanyl)propanoateChEBI
3-MethylthiopropanoateChEBI
3-(Methylsulfanyl)propanoic acidGenerator
3-(Methylsulphanyl)propanoateGenerator
3-(Methylsulphanyl)propanoic acidGenerator
3-Methylthiopropanoic acidGenerator
3-(Methylthio)propionic acidGenerator
3-(methylthio)PropanoateChEBI
3-(methylthio)Propanoic acidGenerator
MMPAMeSH
3-MethylmercaptopropionateMeSH
3-mercapto-2-Methylpropionic acid, monocalcium saltMeSH
3-mercapto-2-Methylpropionic acid, monopotassium saltMeSH
3-MethylthiopropionateMeSH
3-Methylthiopropionate sodium saltMeSH
3-Methylthiopropionic acidMeSH
3-mercapto-2-Methylpropionic acidMeSH
3-mercapto-2-MethylpropionateMeSH
3-mercapto-2-Methylpropionic acid, monosodium saltMeSH
3-S-Methylmercaptopropionic acidGenerator
Chemical FormulaC4H7O2S
Average Molecular Weight119.16
Monoisotopic Molecular Weight119.017224219
IUPAC Name3-(methylsulfanyl)propanoate
Traditional Name3-methylthiopropionate
CAS Registry NumberNot Available
SMILES
CSCCC([O-])=O
InChI Identifier
InChI=1S/C4H8O2S/c1-7-3-2-4(5)6/h2-3H2,1H3,(H,5,6)/p-1
InChI KeyCAOMCZAIALVUPA-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as straight chain fatty acids. These are fatty acids with a straight aliphatic chain.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentStraight chain fatty acids
Alternative Parents
Substituents
  • Straight chain fatty acid
  • Dialkylthioether
  • Sulfenyl compound
  • Thioether
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organosulfur compound
  • Organooxygen compound
  • Carbonyl group
  • 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
logP0.37ALOGPS
logP0.83ChemAxon
logS-0.57ALOGPS
pKa (Strongest Acidic)4.68ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.13 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity40.56 m³·mol⁻¹ChemAxon
Polarizability11.8 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]+127.09332859911
AllCCS[M+H-H2O]+122.92932859911
AllCCS[M+Na]+132.09532859911
AllCCS[M+NH4]+130.97532859911
AllCCS[M-H]-131.52132859911
AllCCS[M+Na-2H]-135.36332859911
AllCCS[M+HCOO]-139.60232859911
DeepCCS[M+H]+132.32330932474
DeepCCS[M-H]-129.85430932474
DeepCCS[M-2H]-166.47130932474
DeepCCS[M+Na]+140.87730932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.4022 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.13 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1519.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid405.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid136.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid284.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid161.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid378.5 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid513.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)210.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid890.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid320.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid970.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid317.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid332.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate485.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA319.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water133.6 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-S-methylmercaptopropionate 10V, Negative-QTOFsplash10-01ba-9500000000-b99f06bbf801bb36c12d2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-S-methylmercaptopropionate 20V, Negative-QTOFsplash10-0002-9200000000-af499e35daa17287a4cf2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-S-methylmercaptopropionate 40V, Negative-QTOFsplash10-0002-9000000000-6f353f3ebeb29d96566c2019-02-23Wishart 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 IDFDB030463
KNApSAcK IDNot Available
Chemspider ID5360205
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID49016
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