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Showing metabocard for 2,3-Dimethylthiophene (HMDB0032977)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:53:03 UTC
Update Date2023-02-21 17:22:55 UTC
HMDB IDHMDB0032977
Secondary Accession Numbers
  • HMDB32977
Metabolite Identification
Common Name2,3-Dimethylthiophene
Description2,3-Dimethylthiophene belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom. 2,3-Dimethylthiophene has been detected, but not quantified in, garden onions (Allium cepa). This could make 2,3-dimethylthiophene a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 2,3-Dimethylthiophene.
Structure
Data?1677000175
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032977 (2,3-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  0  0  0  0            999 V2000
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
Download

3D MOL for HMDB0032977 (2,3-Dimethylthiophene)

HMDB0032977
     RDKit          3D
2,3-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.1890    1.6843    0.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3829    0.2829    0.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7099    0.0154    0.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0971   -1.2746   -0.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6285   -2.0774   -0.3743 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4432   -0.7670   -0.2085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9523   -0.7291   -0.3471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2799    2.1993   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1591    1.5863    0.8175 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5060    2.2466    0.9731 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4962    0.7783    0.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1296   -1.6831   -0.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2693    0.0742   -1.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2314   -1.7389   -0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4260   -0.5972    0.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  2  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
Download

3D SDF for HMDB0032977 (2,3-Dimethylthiophene)


  Mrv0541 05061306502D          

  7  7  0  0  0  0            999 V2000
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  6  5  2  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032977

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=C(C)C=CS1

> <INCHI_IDENTIFIER>
InChI=1S/C6H8S/c1-5-3-4-7-6(5)2/h3-4H,1-2H3

> <INCHI_KEY>
BZYUMXXOAYSFOW-UHFFFAOYSA-N

> <FORMULA>
C6H8S

> <MOLECULAR_WEIGHT>
112.193

> <EXACT_MASS>
112.034670946

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
12.665043597629968

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dimethylthiophene

> <ALOGPS_LOGP>
2.70

> <JCHEM_LOGP>
2.9129699676666667

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.818305237867617

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
33.2613

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.37e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiophene, 2,3-dimethyl-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0032977 (2,3-Dimethylthiophene)

HMDB0032977
     RDKit          3D
2,3-Dimethylthiophene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.1890    1.6843    0.3209 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3829    0.2829    0.0879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7099    0.0154    0.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0971   -1.2746   -0.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6285   -2.0774   -0.3743 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4432   -0.7670   -0.2085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9523   -0.7291   -0.3471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2799    2.1993   -0.6506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1591    1.5863    0.8175 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5060    2.2466    0.9731 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4962    0.7783    0.3950 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1296   -1.6831   -0.0504 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2693    0.0742   -1.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2314   -1.7389   -0.6972 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4260   -0.5972    0.6449 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  2  2  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0032977 (2,3-Dimethylthiophene)

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      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  S   UNK     0       2.306   1.175   0.000  0.00  0.00           S+0
CONECT    1    5                                                            
CONECT    2    6                                                            
CONECT    3    4    5                                                       
CONECT    4    3    7                                                       
CONECT    5    1    3    6                                                  
CONECT    6    2    5    7                                                  
CONECT    7    4    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0032977 (2,3-Dimethylthiophene)

COMPND    HMDB0032977
HETATM    1  C1  UNL     1      -0.189   1.684   0.321  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.383   0.283   0.088  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.710   0.015   0.162  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.097  -1.275  -0.066  1.00  0.00           C  
HETATM    5  S1  UNL     1       0.628  -2.077  -0.374  1.00  0.00           S  
HETATM    6  C5  UNL     1      -0.443  -0.767  -0.208  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.952  -0.729  -0.347  1.00  0.00           C  
HETATM    8  H1  UNL     1      -0.280   2.199  -0.651  1.00  0.00           H  
HETATM    9  H2  UNL     1      -1.159   1.586   0.817  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.506   2.247   0.973  1.00  0.00           H  
HETATM   11  H4  UNL     1       2.496   0.778   0.395  1.00  0.00           H  
HETATM   12  H5  UNL     1       3.130  -1.683  -0.050  1.00  0.00           H  
HETATM   13  H6  UNL     1      -2.269   0.074  -1.006  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.231  -1.739  -0.697  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.426  -0.597   0.645  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    6    6
CONECT    3    4    4   11
CONECT    4    5   12
CONECT    5    6
CONECT    6    7
CONECT    7   13   14   15
END
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SMILES for HMDB0032977 (2,3-Dimethylthiophene)

CC1=C(C)C=CS1
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INCHI for HMDB0032977 (2,3-Dimethylthiophene)

InChI=1S/C6H8S/c1-5-3-4-7-6(5)2/h3-4H,1-2H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2,3-Dimethyl-thiopheneHMDB
Chemical FormulaC6H8S
Average Molecular Weight112.193
Monoisotopic Molecular Weight112.034670946
IUPAC Name2,3-dimethylthiophene
Traditional Namethiophene, 2,3-dimethyl-
CAS Registry Number632-16-6
SMILES
CC1=C(C)C=CS1
InChI Identifier
InChI=1S/C6H8S/c1-5-3-4-7-6(5)2/h3-4H,1-2H3
InChI KeyBZYUMXXOAYSFOW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as heteroaromatic compounds. Heteroaromatic compounds are compounds containing an aromatic ring where a carbon atom is linked to an hetero atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassHeteroaromatic compounds
Sub ClassNot Available
Direct ParentHeteroaromatic compounds
Alternative Parents
Substituents
  • Heteroaromatic compound
  • Thiophene
  • Hydrocarbon derivative
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-49 °CNot Available
Boiling Point138.00 to 140.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility351.5 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.502 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.54 g/LALOGPS
logP2.7ALOGPS
logP2.91ChemAxon
logS-2.3ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.26 m³·mol⁻¹ChemAxon
Polarizability12.67 ųChemAxon
Number of Rings1ChemAxon
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]+119.15531661259
DarkChem[M-H]-112.86531661259
DeepCCS[M+H]+129.58330932474
DeepCCS[M-H]-127.54430932474
DeepCCS[M-2H]-163.11930932474
DeepCCS[M+Na]+137.76330932474
AllCCS[M+H]+117.032859911
AllCCS[M+H-H2O]+112.032859911
AllCCS[M+NH4]+121.632859911
AllCCS[M+Na]+123.032859911
AllCCS[M-H]-119.632859911
AllCCS[M+Na-2H]-122.732859911
AllCCS[M+HCOO]-126.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 4.05 minutes32390414
Predicted by Siyang on May 30, 202215.2743 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.31 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1565.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid593.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid234.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid418.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid277.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid516.6 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 Acid579.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)279.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1227.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid453.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1347.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid448.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid376.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate539.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA431.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water63.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,3-DimethylthiopheneCC1=C(C)C=CS11210.6Standard polar33892256
2,3-DimethylthiopheneCC1=C(C)C=CS1874.1Standard non polar33892256
2,3-DimethylthiopheneCC1=C(C)C=CS1894.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dimethylthiophene GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9800000000-4778c6ca4105115f84852017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Dimethylthiophene 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 - 2,3-Dimethylthiophene 10V, Positive-QTOFsplash10-03di-0900000000-8f50a10d40136a2718872016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 20V, Positive-QTOFsplash10-03di-3900000000-17a3cd95fe8288adb6ce2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 40V, Positive-QTOFsplash10-0uxr-9000000000-0c93e9aa370b082725992016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 10V, Negative-QTOFsplash10-03di-1900000000-214de3d0f4a437aa37b12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 20V, Negative-QTOFsplash10-03di-5900000000-83729934a62adb387bdd2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 40V, Negative-QTOFsplash10-01pt-9000000000-215bba312813ddf501402016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 10V, Positive-QTOFsplash10-03di-2900000000-ab7c5534d27bcfce8bb42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 20V, Positive-QTOFsplash10-0r00-9200000000-7afcaa88a687154040032021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 40V, Positive-QTOFsplash10-0udi-9000000000-acb3640c1f33360645572021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 10V, Negative-QTOFsplash10-06si-9300000000-edcfd529b19003b9ffc22021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 20V, Negative-QTOFsplash10-03di-3900000000-dd2d5c8279529fe7eea52021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Dimethylthiophene 40V, Negative-QTOFsplash10-0bt9-9700000000-d9f75c74f5cea0a4dc562021-09-23Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX 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 IDFDB010964
KNApSAcK IDNot Available
Chemspider ID31595
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound34295
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1580571
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.. .