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Showing metabocard for 1,3-Octadiene (HMDB0040966)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-12 02:35:51 UTC
Update Date2022-03-07 02:56:49 UTC
HMDB IDHMDB0040966
Secondary Accession Numbers
  • HMDB40966
Metabolite Identification
Common Name1,3-Octadiene
Description1,3-Octadiene belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds. 1,3-Octadiene has been detected, but not quantified in, pulses. This could make 1,3-octadiene a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 1,3-Octadiene.
Structure
Data?1563863609
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040966 (1,3-Octadiene)


  Mrv0541 02241218332D          

  8  7  0  0  0  0            999 V2000
   -1.7734   -1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7734   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0308    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3708    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1133   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7734    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7734    1.0305    0.0000 C   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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
Download

3D MOL for HMDB0040966 (1,3-Octadiene)

HMDB0040966
     RDKit          3D
1,3-Octadiene
 22 21  0  0  0  0  0  0  0  0999 V2000
    4.4657   -0.2739    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3326    0.1625   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.3083    0.0572 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9405    0.1731   -0.5122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3924   -0.2521   -0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2618    0.8613    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6002    0.2491    0.8225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2586   -0.4216   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4208    0.0728   -0.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4602   -0.9970    0.8999 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3994    0.8855   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9964   -1.0371    0.8643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9862    0.9035   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2950   -1.0015    0.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9100   -0.6789   -0.9897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8519    1.3455    1.3222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3915    1.5901   -0.4130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3728   -0.5059    1.5950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3001    0.9857    1.2231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2900    0.2585   -1.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7843   -1.4000   -0.5948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3266   -0.6115   -0.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  8 22  1  0
M  END
Download

3D SDF for HMDB0040966 (1,3-Octadiene)


  Mrv0541 02241218332D          

  8  7  0  0  0  0            999 V2000
   -1.7734   -1.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7734   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0308    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3708    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1133   -0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7734    0.2055    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7734    1.0305    0.0000 C   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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040966

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCC\C=C\C=C

> <INCHI_IDENTIFIER>
InChI=1S/C8H14/c1-3-5-7-8-6-4-2/h3,5,7H,1,4,6,8H2,2H3/b7-5+

> <INCHI_KEY>
QTYUSOHYEPOHLV-FNORWQNLSA-N

> <FORMULA>
C8H14

> <MOLECULAR_WEIGHT>
110.1968

> <EXACT_MASS>
110.109550448

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
14.999435107931546

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3E)-octa-1,3-diene

> <ALOGPS_LOGP>
4.19

> <JCHEM_LOGP>
3.3543655796666663

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
39.7709

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.69e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3E)-octa-1,3-diene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0040966 (1,3-Octadiene)

HMDB0040966
     RDKit          3D
1,3-Octadiene
 22 21  0  0  0  0  0  0  0  0999 V2000
    4.4657   -0.2739    0.0982 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3326    0.1625   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0336   -0.3083    0.0572 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9405    0.1731   -0.5122 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3924   -0.2521   -0.0840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2618    0.8613    0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6002    0.2491    0.8225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2586   -0.4216   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4208    0.0728   -0.2552 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4602   -0.9970    0.8999 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3994    0.8855   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9964   -1.0371    0.8643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9862    0.9035   -1.3207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2950   -1.0015    0.7130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9100   -0.6789   -0.9897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8519    1.3455    1.3222 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3915    1.5901   -0.4130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3728   -0.5059    1.5950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3001    0.9857    1.2231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2900    0.2585   -1.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7843   -1.4000   -0.5948 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3266   -0.6115   -0.0686 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
  7 18  1  0
  7 19  1  0
  8 20  1  0
  8 21  1  0
  8 22  1  0
M  END
Download

PDB for HMDB0040966 (1,3-Octadiene)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -3.310  -1.924   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.310  -0.384   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.924   0.384   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.692  -0.384   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.692   0.384   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.078  -0.384   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.310   0.384   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.310   1.924   0.000  0.00  0.00           C+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                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0040966 (1,3-Octadiene)

COMPND    HMDB0040966
HETATM    1  C1  UNL     1       4.466  -0.274   0.098  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.333   0.163  -0.423  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.034  -0.308   0.057  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.941   0.173  -0.512  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.392  -0.252  -0.084  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.262   0.861   0.423  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.600   0.249   0.822  1.00  0.00           C  
HETATM    8  C8  UNL     1      -3.259  -0.422  -0.373  1.00  0.00           C  
HETATM    9  H1  UNL     1       5.421   0.073  -0.255  1.00  0.00           H  
HETATM   10  H2  UNL     1       4.460  -0.997   0.900  1.00  0.00           H  
HETATM   11  H3  UNL     1       3.399   0.885  -1.222  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.996  -1.037   0.864  1.00  0.00           H  
HETATM   13  H5  UNL     1       0.986   0.903  -1.321  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.295  -1.001   0.713  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.910  -0.679  -0.990  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.852   1.345   1.322  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.391   1.590  -0.413  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.373  -0.506   1.595  1.00  0.00           H  
HETATM   19  H11 UNL     1      -3.300   0.986   1.223  1.00  0.00           H  
HETATM   20  H12 UNL     1      -3.290   0.259  -1.240  1.00  0.00           H  
HETATM   21  H13 UNL     1      -2.784  -1.400  -0.595  1.00  0.00           H  
HETATM   22  H14 UNL     1      -4.327  -0.611  -0.069  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    4   12
CONECT    4    5   13
CONECT    5    6   14   15
CONECT    6    7   16   17
CONECT    7    8   18   19
CONECT    8   20   21   22
END
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SMILES for HMDB0040966 (1,3-Octadiene)

CCCC\C=C\C=C
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INCHI for HMDB0040966 (1,3-Octadiene)

InChI=1S/C8H14/c1-3-5-7-8-6-4-2/h3,5,7H,1,4,6,8H2,2H3/b7-5+
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(3E)-1,3-OctadieneHMDB
(e)-1,3-OctadieneHMDB
1,3-Octadiene, eHMDB
1,3-Octadiene, transHMDB
OctadieneHMDB
Chemical FormulaC8H14
Average Molecular Weight110.1968
Monoisotopic Molecular Weight110.109550448
IUPAC Name(3E)-octa-1,3-diene
Traditional Name(3E)-octa-1,3-diene
CAS Registry Number1002-33-1
SMILES
CCCC\C=C\C=C
InChI Identifier
InChI=1S/C8H14/c1-3-5-7-8-6-4-2/h3,5,7H,1,4,6,8H2,2H3/b7-5+
InChI KeyQTYUSOHYEPOHLV-FNORWQNLSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassOlefins
Direct ParentAlkadienes
Alternative Parents
Substituents
  • Alkadiene
  • Unsaturated aliphatic hydrocarbon
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Not AvailableNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point127.00 to 128.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility14.2 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP3.965 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.017 g/LALOGPS
logP4.19ALOGPS
logP3.35ChemAxon
logS-3.8ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity39.77 m³·mol⁻¹ChemAxon
Polarizability15 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]+127.21231661259
DarkChem[M-H]-122.88531661259
DeepCCS[M+H]+129.3230932474
DeepCCS[M-H]-126.59230932474
DeepCCS[M-2H]-163.03330932474
DeepCCS[M+Na]+137.69830932474
AllCCS[M+H]+127.732859911
AllCCS[M+H-H2O]+123.332859911
AllCCS[M+NH4]+131.832859911
AllCCS[M+Na]+133.032859911
AllCCS[M-H]-132.032859911
AllCCS[M+Na-2H]-135.232859911
AllCCS[M+HCOO]-138.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,3-OctadieneCCCC\C=C\C=C942.8Standard polar33892256
1,3-OctadieneCCCC\C=C\C=C825.1Standard non polar33892256
1,3-OctadieneCCCC\C=C\C=C809.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Octadiene GC-MS (Non-derivatized) - 70eV, Positivesplash10-0bvi-9200000000-049fe7b55853e24f04322016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Octadiene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,3-Octadiene 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 - 1,3-Octadiene 10V, Positive-QTOFsplash10-03di-1900000000-cd7ec34db95252912e0a2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 20V, Positive-QTOFsplash10-03di-7900000000-bb3d80ba65996b21ec782016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 40V, Positive-QTOFsplash10-0ktf-9000000000-c7b30c98d60e971563632016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 10V, Negative-QTOFsplash10-0a4i-0900000000-021b70a002fb459488982016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 20V, Negative-QTOFsplash10-0a4i-0900000000-abd13d4b2ab67c0d66992016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 40V, Negative-QTOFsplash10-0a4l-9300000000-232485031f2a85cadbe12016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 10V, Negative-QTOFsplash10-0a4i-0900000000-145993eaa9732cb5e2ad2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 20V, Negative-QTOFsplash10-0a4i-0900000000-145993eaa9732cb5e2ad2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 40V, Negative-QTOFsplash10-0gba-9000000000-0b7ea9e1f0ebd31ee8a12021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 10V, Positive-QTOFsplash10-0api-9100000000-be2b9cf27e87b8c3aa3b2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 20V, Positive-QTOFsplash10-0pw9-9000000000-4ca3732d5c05ea48cc002021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,3-Octadiene 40V, Positive-QTOFsplash10-0uxr-9000000000-0ad3ace94222f519f6542021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB020820
KNApSAcK IDC00056790
Chemspider ID451647
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound517653
PDB IDNot Available
ChEBI ID89638
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1603341
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.. .