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Showing metabocard for 1-Pentanesulfenothioic acid (HMDB0031160)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:41:21 UTC
Update Date2023-02-21 17:19:56 UTC
HMDB IDHMDB0031160
Secondary Accession Numbers
  • HMDB31160
Metabolite Identification
Common Name1-Pentanesulfenothioic acid
Description1-Pentanesulfenothioic acid, also known as 1-pentanesulphenothioate, belongs to the class of organic compounds known as sulfenyl compounds. These are organosulfur compounds a sulfenyl group with the general formula RS (R = organyl). 1-Pentanesulfenothioic acid is found, on average, in the highest concentration within chives (Allium schoenoprasum). 1-Pentanesulfenothioic acid has also been detected, but not quantified in, several different foods, such as welsh onions (Allium fistulosum), green onion, garden onion (var.), garden onions (Allium cepa), and onion-family vegetables. This could make 1-pentanesulfenothioic acid a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 1-Pentanesulfenothioic acid.
Structure
Data?1676999996
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031160 (1-Pentanesulfenothioic acid)


  Mrv0541 05061305462D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   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
    6.0474    1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031160 (1-Pentanesulfenothioic acid)

HMDB0031160
     RDKit          3D
1-Pentanesulfenothioic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2601    0.5194   -0.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5840   -0.7857   -0.2116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4711   -0.6895    0.7670 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6335    0.2313    0.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2381   -0.2532   -1.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5478    0.9641   -1.4346 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.0327    0.7227    0.1006 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9527    0.3379   -1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5497    1.2951   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9040    0.8838    0.3118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2050   -1.2029   -1.1659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3750   -1.4689    0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0028   -1.7136    0.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7685   -0.4390    1.7879 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2661    1.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2131    1.2451    0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7429   -1.2280   -0.8622 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4809   -0.2687   -1.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7495    1.5839    1.1830 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  7 19  1  0
M  END
Download

3D SDF for HMDB0031160 (1-Pentanesulfenothioic acid)


  Mrv0541 05061305462D          

  7  6  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   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
    6.0474    1.8414    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031160

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCSS

> <INCHI_IDENTIFIER>
InChI=1S/C5H12S2/c1-2-3-4-5-7-6/h6H,2-5H2,1H3

> <INCHI_KEY>
DPLYGYOSWLFGGY-UHFFFAOYSA-N

> <FORMULA>
C5H12S2

> <MOLECULAR_WEIGHT>
136.279

> <EXACT_MASS>
136.038041764

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
16.151432701305996

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentane-1-dithioperoxol

> <ALOGPS_LOGP>
2.99

> <JCHEM_LOGP>
2.9397510906666664

> <ALOGPS_LOGS>
-2.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.45904077633399

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
38.5762

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentane-1-dithioperoxol

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031160 (1-Pentanesulfenothioic acid)

HMDB0031160
     RDKit          3D
1-Pentanesulfenothioic acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2601    0.5194   -0.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5840   -0.7857   -0.2116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4711   -0.6895    0.7670 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6335    0.2313    0.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2381   -0.2532   -1.0163 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5478    0.9641   -1.4346 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.0327    0.7227    0.1006 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9527    0.3379   -1.3718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5497    1.2951   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9040    0.8838    0.3118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2050   -1.2029   -1.1659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3750   -1.4689    0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0028   -1.7136    0.8201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7685   -0.4390    1.7879 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.2661    1.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2131    1.2451    0.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7429   -1.2280   -0.8622 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4809   -0.2687   -1.8114 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7495    1.5839    1.1830 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
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  7 19  1  0
M  END
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PDB for HMDB0031160 (1-Pentanesulfenothioic acid)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0      11.288   3.437   0.000  0.00  0.00           S+0
HETATM    7  S   UNK     0       9.955   2.667   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    7                                                       
CONECT    6    7                                                            
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0031160 (1-Pentanesulfenothioic acid)

COMPND    HMDB0031160
HETATM    1  C1  UNL     1      -2.260   0.519  -0.515  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.584  -0.786  -0.212  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.471  -0.689   0.767  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.633   0.231   0.296  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.238  -0.253  -1.016  1.00  0.00           C  
HETATM    6  S1  UNL     1       2.548   0.964  -1.435  1.00  0.00           S  
HETATM    7  S2  UNL     1       4.033   0.723   0.101  1.00  0.00           S  
HETATM    8  H1  UNL     1      -2.953   0.338  -1.372  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.550   1.295  -0.862  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.904   0.884   0.312  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.205  -1.203  -1.166  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.375  -1.469   0.191  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.003  -1.714   0.820  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.768  -0.439   1.788  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.429   0.266   1.083  1.00  0.00           H  
HETATM   16  H9  UNL     1       0.213   1.245   0.199  1.00  0.00           H  
HETATM   17  H10 UNL     1       1.743  -1.228  -0.862  1.00  0.00           H  
HETATM   18  H11 UNL     1       0.481  -0.269  -1.811  1.00  0.00           H  
HETATM   19  H12 UNL     1       3.749   1.584   1.183  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7
CONECT    7   19
END
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SMILES for HMDB0031160 (1-Pentanesulfenothioic acid)

CCCCCSS
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INCHI for HMDB0031160 (1-Pentanesulfenothioic acid)

InChI=1S/C5H12S2/c1-2-3-4-5-7-6/h6H,2-5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-PentanesulfenothioateGenerator
1-PentanesulphenothioateGenerator
1-Pentanesulphenothioic acidGenerator
Pentyl hydrodisulfideHMDB
Chemical FormulaC5H12S2
Average Molecular Weight136.279
Monoisotopic Molecular Weight136.038041764
IUPAC Namepentane-1-dithioperoxol
Traditional Namepentane-1-dithioperoxol
CAS Registry Number86849-52-7
SMILES
CCCCCSS
InChI Identifier
InChI=1S/C5H12S2/c1-2-3-4-5-7-6/h6H,2-5H2,1H3
InChI KeyDPLYGYOSWLFGGY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as sulfenyl compounds. These are organosulfur compounds a sulfenyl group with the general formula RS (R = organyl).
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassSulfenyl compounds
Sub ClassNot Available
Direct ParentSulfenyl compounds
Alternative Parents
Substituents
  • Sulfenyl compound
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point172.91 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility134.4 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP3.900 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.24 g/LALOGPS
logP2.99ALOGPS
logP2.94ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)9.46ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity38.58 m³·mol⁻¹ChemAxon
Polarizability16.15 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.06431661259
DarkChem[M-H]-124.56631661259
DeepCCS[M+H]+137.88830932474
DeepCCS[M-H]-135.72130932474
DeepCCS[M-2H]-171.35330932474
DeepCCS[M+Na]+145.96830932474
AllCCS[M+H]+130.832859911
AllCCS[M+H-H2O]+126.732859911
AllCCS[M+NH4]+134.632859911
AllCCS[M+Na]+135.732859911
AllCCS[M-H]-143.132859911
AllCCS[M+Na-2H]-147.032859911
AllCCS[M+HCOO]-151.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-Pentanesulfenothioic acidCCCCCSS1504.1Standard polar33892256
1-Pentanesulfenothioic acidCCCCCSS1062.9Standard non polar33892256
1-Pentanesulfenothioic acidCCCCCSS1070.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-Pentanesulfenothioic acid,1TMS,isomer #1CCCCCSS[Si](C)(C)C1266.3Semi standard non polar33892256
1-Pentanesulfenothioic acid,1TMS,isomer #1CCCCCSS[Si](C)(C)C1272.5Standard non polar33892256
1-Pentanesulfenothioic acid,1TBDMS,isomer #1CCCCCSS[Si](C)(C)C(C)(C)C1526.6Semi standard non polar33892256
1-Pentanesulfenothioic acid,1TBDMS,isomer #1CCCCCSS[Si](C)(C)C(C)(C)C1487.5Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - 1-Pentanesulfenothioic acid EI-B (Non-derivatized)splash10-00dr-9800000000-d326095cea1b844980822017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - 1-Pentanesulfenothioic acid EI-B (Non-derivatized)splash10-00dr-9800000000-d326095cea1b844980822018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Pentanesulfenothioic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-004l-9100000000-b6aaf9294b18dfc8cc782017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Pentanesulfenothioic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 10V, Positive-QTOFsplash10-00dr-9800000000-b8729d9a48b24952c5b62015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 20V, Positive-QTOFsplash10-000i-6900000000-2612eb031cd486e9f6162015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 40V, Positive-QTOFsplash10-05fu-9000000000-a94e1002ed9d6fa5f1f72015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 10V, Negative-QTOFsplash10-0079-9800000000-221cc4e1c0279a4abbc52015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 20V, Negative-QTOFsplash10-0079-9600000000-40eea5137f4c84742ecc2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 40V, Negative-QTOFsplash10-07rr-9000000000-a9d69dff7cee2acce9fd2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 10V, Negative-QTOFsplash10-03di-9400000000-80d36cc5fbd59436d0bf2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 20V, Negative-QTOFsplash10-03di-9200000000-10d4d419ea7d5ffc17072021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 40V, Negative-QTOFsplash10-03di-9000000000-bda92f13cfa445b061602021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 10V, Positive-QTOFsplash10-0udi-5900000000-e606094dbb40100409e52021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 20V, Positive-QTOFsplash10-014l-9100000000-04be510728fb81dfd1822021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Pentanesulfenothioic acid 40V, Positive-QTOFsplash10-06r2-9000000000-4421cbddf5e968bc04df2021-09-25Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Membrane
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 IDFDB003175
KNApSAcK IDC00057611
Chemspider ID13627664
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound21251947
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1630991
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .