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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 21:50:43 UTC

Update Date

2022-03-07 02:55:01 UTC

HMDB ID

HMDB0036678

Secondary Accession Numbers

HMDB36678

Metabolite Identification

Common Name

alpha-Bergamotene

Description

alpha-Bergamotene, also known as α-bergamotene, belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other. Based on a literature review a small amount of articles have been published on alpha-Bergamotene.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0036678
     RDKit          3D
alpha-Bergamotene
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.8144    0.8143    0.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3726   -0.4241    0.1828 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3554   -1.3146   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0572   -0.6907    0.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0695    0.1935    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0788    0.8578   -0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8385    0.0329   -0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2101   -0.8723   -1.8696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.7624   -1.4549 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5986    1.7992   -0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9545    1.1975    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4363    0.0131    1.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4134   -0.5426    2.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8639   -0.7749   -0.0653 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8026   -0.5244   -1.2501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6025    0.7096    1.9743 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3090    1.7183    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9191    0.9547    0.7392 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3691   -1.0754   -0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3089   -1.1302   -1.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1563   -2.3884   -0.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7594   -1.5979   -0.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6603    0.9514    1.4255 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5715   -0.4227    1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4320    1.6373    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6690    1.4866   -0.7941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1708   -1.9403   -1.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8324   -0.8793   -2.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8137   -0.5705   -2.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9236    1.0354   -2.5044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5157    2.1950   -1.0172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    2.6657   -0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6096    1.7297    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3132   -1.1954    2.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3446    0.2517    3.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5226   -1.2224    2.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6145   -1.8131    0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6746   -1.2518   -2.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8597   -0.3747   -0.9431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14  7  1  0
 15  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  6
 10 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 13 36  1  0
 14 37  1  1
 15 38  1  0
 15 39  1  0
M  END


  Mrv0541 02241212582D          

 15 16  0  0  0  0            999 V2000
   -2.9188    2.0331    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2044    1.6205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2044    0.7955    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9188    0.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6333    0.7955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6333    1.6205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2044    2.4455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4899    2.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7754    1.6205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0610    2.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6535    1.6205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3680    2.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6535    0.7955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9188    1.2080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3478    2.0330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  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
  2  7  1  0  0  0  0
  2  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  3 14  1  1  0  0  0
  1 14  1  1  0  0  0
  6 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036678

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC1(C)[C@H]2C[C@@H]1C(C)=CC2

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11(2)6-5-9-15(4)13-8-7-12(3)14(15)10-13/h6-7,13-14H,5,8-10H2,1-4H3/t13-,14-,15?/m1/s1

> <INCHI_KEY>
YMBFCQPIMVLNIU-GRKKQISMSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.3511

> <EXACT_MASS>
204.187800768

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
26.576364696351447

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,5R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

> <ALOGPS_LOGP>
5.91

> <JCHEM_LOGP>
4.461375721333334

> <ALOGPS_LOGS>
-4.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
68.5249

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.82e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,5R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0036678
     RDKit          3D
alpha-Bergamotene
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.8144    0.8143    0.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3726   -0.4241    0.1828 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3554   -1.3146   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0572   -0.6907    0.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0695    0.1935    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0788    0.8578   -0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8385    0.0329   -0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2101   -0.8723   -1.8696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.7624   -1.4549 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5986    1.7992   -0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9545    1.1975    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4363    0.0131    1.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4134   -0.5426    2.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8639   -0.7749   -0.0653 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8026   -0.5244   -1.2501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6025    0.7096    1.9743 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3090    1.7183    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9191    0.9547    0.7392 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3691   -1.0754   -0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3089   -1.1302   -1.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1563   -2.3884   -0.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7594   -1.5979   -0.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6603    0.9514    1.4255 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5715   -0.4227    1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4320    1.6373    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6690    1.4866   -0.7941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1708   -1.9403   -1.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8324   -0.8793   -2.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8137   -0.5705   -2.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9236    1.0354   -2.5044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5157    2.1950   -1.0172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    2.6657   -0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6096    1.7297    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3132   -1.1954    2.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3446    0.2517    3.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5226   -1.2224    2.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6145   -1.8131    0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6746   -1.2518   -2.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8597   -0.3747   -0.9431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14  7  1  0
 15  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  6
 10 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 13 36  1  0
 14 37  1  1
 15 38  1  0
 15 39  1  0
M  END

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      -5.448   3.795   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.115   3.025   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.115   1.485   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.448   0.715   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -6.782   1.485   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -6.782   3.025   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.115   4.565   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.781   3.795   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.447   3.025   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.114   3.795   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.220   3.025   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.554   3.795   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.220   1.485   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.448   2.255   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -8.116   3.795   0.000  0.00  0.00           C+0
CONECT    1    2    6   14                                                  
CONECT    2    1    3    7    8                                             
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5   15                                                  
CONECT    7    2                                                            
CONECT    8    2    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    3    1                                                       
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0036678
HETATM    1  C1  UNL     1       3.814   0.814   0.877  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.373  -0.424   0.183  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.355  -1.315  -0.465  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.057  -0.691   0.173  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.069   0.193   0.817  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.079   0.858  -0.049  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.838   0.033  -0.852  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.210  -0.872  -1.870  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.029   0.762  -1.455  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.599   1.799  -0.538  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.955   1.197   0.790  1.00  0.00           C  
HETATM   12  C12 UNL     1      -2.436   0.013   1.048  1.00  0.00           C  
HETATM   13  C13 UNL     1      -2.413  -0.543   2.414  1.00  0.00           C  
HETATM   14  C14 UNL     1      -1.864  -0.775  -0.065  1.00  0.00           C  
HETATM   15  C15 UNL     1      -2.803  -0.524  -1.250  1.00  0.00           C  
HETATM   16  H1  UNL     1       3.602   0.710   1.974  1.00  0.00           H  
HETATM   17  H2  UNL     1       3.309   1.718   0.519  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.919   0.955   0.739  1.00  0.00           H  
HETATM   19  H4  UNL     1       5.369  -1.075  -0.099  1.00  0.00           H  
HETATM   20  H5  UNL     1       4.309  -1.130  -1.566  1.00  0.00           H  
HETATM   21  H6  UNL     1       4.156  -2.388  -0.249  1.00  0.00           H  
HETATM   22  H7  UNL     1       1.759  -1.598  -0.314  1.00  0.00           H  
HETATM   23  H8  UNL     1       1.660   0.951   1.426  1.00  0.00           H  
HETATM   24  H9  UNL     1       0.571  -0.423   1.634  1.00  0.00           H  
HETATM   25  H10 UNL     1      -0.432   1.637   0.566  1.00  0.00           H  
HETATM   26  H11 UNL     1       0.669   1.487  -0.794  1.00  0.00           H  
HETATM   27  H12 UNL     1      -0.171  -1.940  -1.581  1.00  0.00           H  
HETATM   28  H13 UNL     1      -0.832  -0.879  -2.827  1.00  0.00           H  
HETATM   29  H14 UNL     1       0.814  -0.571  -2.172  1.00  0.00           H  
HETATM   30  H15 UNL     1      -1.924   1.035  -2.504  1.00  0.00           H  
HETATM   31  H16 UNL     1      -3.516   2.195  -1.017  1.00  0.00           H  
HETATM   32  H17 UNL     1      -1.927   2.666  -0.380  1.00  0.00           H  
HETATM   33  H18 UNL     1      -3.610   1.730   1.489  1.00  0.00           H  
HETATM   34  H19 UNL     1      -3.313  -1.195   2.604  1.00  0.00           H  
HETATM   35  H20 UNL     1      -2.345   0.252   3.196  1.00  0.00           H  
HETATM   36  H21 UNL     1      -1.523  -1.222   2.491  1.00  0.00           H  
HETATM   37  H22 UNL     1      -1.614  -1.813   0.124  1.00  0.00           H  
HETATM   38  H23 UNL     1      -2.675  -1.252  -2.073  1.00  0.00           H  
HETATM   39  H24 UNL     1      -3.860  -0.375  -0.943  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    4    4
CONECT    3   19   20   21
CONECT    4    5   22
CONECT    5    6   23   24
CONECT    6    7   25   26
CONECT    7    8    9   14
CONECT    8   27   28   29
CONECT    9   10   15   30
CONECT   10   11   31   32
CONECT   11   12   12   33
CONECT   12   13   14
CONECT   13   34   35   36
CONECT   14   15   37
CONECT   15   38   39
END

HMDB0036678
     RDKit          3D
alpha-Bergamotene
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.8144    0.8143    0.8768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3726   -0.4241    0.1828 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3554   -1.3146   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0572   -0.6907    0.1729 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0695    0.1935    0.8172 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0788    0.8578   -0.0494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8385    0.0329   -0.8520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2101   -0.8723   -1.8696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0287    0.7624   -1.4549 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5986    1.7992   -0.5379 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9545    1.1975    0.7897 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4363    0.0131    1.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4134   -0.5426    2.4136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8639   -0.7749   -0.0653 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8026   -0.5244   -1.2501 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6025    0.7096    1.9743 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3090    1.7183    0.5186 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9191    0.9547    0.7392 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3691   -1.0754   -0.0988 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3089   -1.1302   -1.5660 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1563   -2.3884   -0.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7594   -1.5979   -0.3141 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6603    0.9514    1.4255 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5715   -0.4227    1.6339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4320    1.6373    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6690    1.4866   -0.7941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1708   -1.9403   -1.5808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8324   -0.8793   -2.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8137   -0.5705   -2.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9236    1.0354   -2.5044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5157    2.1950   -1.0172 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9270    2.6657   -0.3801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6096    1.7297    1.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3132   -1.1954    2.6037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3446    0.2517    3.1964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5226   -1.2224    2.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6145   -1.8131    0.1239 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6746   -1.2518   -2.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8597   -0.3747   -0.9431 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14  7  1  0
 15  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  3 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  6 26  1  0
  8 27  1  0
  8 28  1  0
  8 29  1  0
  9 30  1  6
 10 31  1  0
 10 32  1  0
 11 33  1  0
 13 34  1  0
 13 35  1  0
 13 36  1  0
 14 37  1  1
 15 38  1  0
 15 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
a-Bergamotene	Generator
Α-bergamotene	Generator
Bergamotene	HMDB

Chemical Formula

C₁₅H₂₄

Average Molecular Weight

204.3511

Monoisotopic Molecular Weight

204.187800768

IUPAC Name

(1R,5R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

Traditional Name

(1R,5R)-2,6-dimethyl-6-(4-methylpent-3-en-1-yl)bicyclo[3.1.1]hept-2-ene

CAS Registry Number

13474-59-4

SMILES

CC(C)=CCCC1(C)[C@H]2C[C@@H]1C(C)=CC2

InChI Identifier

InChI=1S/C15H24/c1-11(2)6-5-9-15(4)13-8-7-12(3)14(15)10-13/h6-7,13-14H,5,8-10H2,1-4H3/t13-,14-,15?/m1/s1

InChI Key

YMBFCQPIMVLNIU-GRKKQISMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Bicyclic monoterpenoids

Alternative Parents

Substituents

Pinane monoterpenoid
Bicyclic monoterpenoid
Branched unsaturated hydrocarbon
Polycyclic hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Cytoplasm (HMDB: HMDB0036678)
Cell membrane (HMDB: HMDB0036678)

Biofluid or Excreta

Feces (HMDB: HMDB0036678)

Excreta

Biofluid or Excreta

Feces (PMID: 17314143)

Cellular substructure

Extracellular (HMDB: HMDB0036678)
Membrane (HMDB: HMDB0036678)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036678)

Source

Endogenous

Endogenous (HMDB: HMDB0036678)

Plant

Plant (HMDB: HMDB0036678)

Animal

Animal (HMDB: HMDB0036678)

Exogenous

Food

Food (HMDB: HMDB0036678)

Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Sweet orange (FooDB: FOOD00057)
Citrus (FooDB: FOOD00859)

Herb and spice

Spice

Nutmeg (FooDB: FOOD00118)

Herb

Sweet basil (FooDB: FOOD00119)

Fat and oil

Fats and oils (FooDB: FOOD00864)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid peroxidation (HMDB: HMDB0036678)

Biochemical process

Fatty acid metabolism (HMDB: HMDB0036678)

Cellular process

Cell signaling (HMDB: HMDB0036678)

Biochemical pathway

Lipid metabolism pathway (HMDB: HMDB0036678)

Role

Biological role

Membrane stabilizer (HMDB: HMDB0036678)

Nutrient

Nutrient (HMDB: HMDB0036678)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036678)

Emulsifier (HMDB: HMDB0036678)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	259.00 to 260.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	0.03 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	6.540 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0068 g/L	ALOGPS
logP	5.91	ALOGPS
logP	4.46	ChemAxon
logS	-4.5	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	68.52 m³·mol⁻¹	ChemAxon
Polarizability	26.58 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	152.528	31661259
DarkChem	[M-H]-	148.41	31661259
DeepCCS	[M+H]+	155.246	30932474
DeepCCS	[M-H]-	152.888	30932474
DeepCCS	[M-2H]-	186.007	30932474
DeepCCS	[M+Na]+	161.339	30932474
AllCCS	[M+H]+	148.8	32859911
AllCCS	[M+H-H2O]+	145.0	32859911
AllCCS	[M+NH4]+	152.4	32859911
AllCCS	[M+Na]+	153.5	32859911
AllCCS	[M-H]-	158.3	32859911
AllCCS	[M+Na-2H]-	158.9	32859911
AllCCS	[M+HCOO]-	159.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
alpha-Bergamotene	CC(C)=CCCC1(C)[C@H]2C[C@@H]1C(C)=CC2	1601.6	Standard polar	33892256
alpha-Bergamotene	CC(C)=CCCC1(C)[C@H]2C[C@@H]1C(C)=CC2	1458.0	Standard non polar	33892256
alpha-Bergamotene	CC(C)=CCCC1(C)[C@H]2C[C@@H]1C(C)=CC2	1453.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - alpha-Bergamotene GC-MS (Non-derivatized) - 70eV, Positive	splash10-00kf-9300000000-43645492e289cb9cf876	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - alpha-Bergamotene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 10V, Positive-QTOF	splash10-0a4i-1390000000-d6a0ba11c5a26587cd86	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 20V, Positive-QTOF	splash10-0aor-4940000000-9dc882467486d9fdf061	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 40V, Positive-QTOF	splash10-014i-5900000000-ea9024d4d9b8c46f7756	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 10V, Negative-QTOF	splash10-0udi-0090000000-1d073790940a713722d2	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 20V, Negative-QTOF	splash10-0udi-0090000000-de5ae459f3052d9744b7	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 40V, Negative-QTOF	splash10-0fy9-3910000000-729cba2ca70dcf19f20f	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 10V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 20V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 40V, Negative-QTOF	splash10-0uxr-0790000000-5f2697dd150bf0825ae5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 10V, Positive-QTOF	splash10-060r-2920000000-b37f23a73e76ccb77633	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 20V, Positive-QTOF	splash10-00di-3900000000-bdedd611b0ff9d625863	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - alpha-Bergamotene 40V, Positive-QTOF	splash10-069r-9000000000-b2a695a52a29c98c4260	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Feces

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	17314143	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB015608

KNApSAcK ID

C00021903

Chemspider ID

35014195

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Bergamotene

METLIN ID

Not Available

PubChem Compound

91753502

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1384461

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for alpha-Bergamotene (HMDB0036678)

MOL for HMDB0036678 (alpha-Bergamotene)

3D MOL for HMDB0036678 (alpha-Bergamotene)

3D SDF for HMDB0036678 (alpha-Bergamotene)

3D-SDF for HMDB0036678 (alpha-Bergamotene)

PDB for HMDB0036678 (alpha-Bergamotene)

3D PDB for HMDB0036678 (alpha-Bergamotene)

SMILES for HMDB0036678 (alpha-Bergamotene)

INCHI for HMDB0036678 (alpha-Bergamotene)

Structure for HMDB0036678 (alpha-Bergamotene)

3D Structure for HMDB0036678 (alpha-Bergamotene)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra