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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 23:25:12 UTC

Update Date

2022-03-07 02:55:38 UTC

HMDB ID

HMDB0038137

Secondary Accession Numbers

HMDB38137

Metabolite Identification

Common Name

Bicyclogermacrene

Description

Bicyclogermacrene belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]undecane, 9CI) skeleton or the isolepidozane skeleton. Based on a literature review a significant number of articles have been published on Bicyclogermacrene.

Structure

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

HMDB0038137
     RDKit          3D
Bicyclogermacrene
 39 40  0  0  0  0  0  0  0  0999 V2000
   -1.3386    2.4194   -0.9562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4640    1.7158    0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7279    1.2486   -0.3290 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6122    0.5494    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2884   -0.8695    0.7291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2234   -1.3820   -0.1874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142   -1.5299    0.5146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1889   -0.8312   -0.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6300   -1.4457   -1.5442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7475    0.2907    0.1895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3150    0.9032    1.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9688    1.5479    1.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5693   -0.4545    0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8024   -0.5372   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8033   -0.8035    0.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0856    3.0238   -0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6808    3.1229   -1.5190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7463    1.7117   -1.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0551    1.3934   -1.3498 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9471    1.1525    1.4684 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2915   -1.2955    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1330   -0.7386   -1.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5802   -2.3785   -0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1846    1.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3377   -2.6337    0.5847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8140   -0.6611   -2.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5742   -1.9973   -1.3591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8470   -2.1076   -1.9317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5240    0.7407   -0.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0598    1.7100    1.7346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4007    0.1741    2.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2032    1.0058    2.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9815    2.5867    1.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2511   -1.5354   -1.6377 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5885    0.2113   -1.6282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9238   -0.3477   -1.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6906   -0.3660    0.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9144   -1.9076    0.8448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6911   -0.5008    1.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
  5 13  1  0
 13 14  1  0
 13 15  1  0
 12  2  1  0
 13  4  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END


  Mrv0541 05061310152D          

 15 16  0  0  0  0            999 V2000
    2.9789    3.1363    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0392   -0.5257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4021    2.2389    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9420    1.0960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7439    0.9662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0963    1.7122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9217    0.8984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8043    2.3225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4519    1.5766    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7471    0.0847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6265    2.3903    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5694    0.1525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297    1.5088    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2773    0.7628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1925    1.4409    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  8  1  0  0  0  0
 11  1  1  0  0  0  0
 11  6  2  0  0  0  0
 11  8  1  0  0  0  0
 12  2  1  0  0  0  0
 12  7  1  0  0  0  0
 12 10  2  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 14 13  1  0  0  0  0
 15  3  1  0  0  0  0
 15  4  1  0  0  0  0
 15 13  1  0  0  0  0
 15 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038137

> <DATABASE_NAME>
hmdb

> <SMILES>
C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-11-6-5-7-12(2)10-14-13(9-8-11)15(14,3)4/h6,10,13-14H,5,7-9H2,1-4H3/b11-6-,12-10-

> <INCHI_KEY>
VPDZRSSKICPUEY-SUYBHAEQSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.3511

> <EXACT_MASS>
204.187800768

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
25.906456150620244

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

> <ALOGPS_LOGP>
5.09

> <JCHEM_LOGP>
4.461375721333334

> <ALOGPS_LOGS>
-4.39

> <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>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.37e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0038137
     RDKit          3D
Bicyclogermacrene
 39 40  0  0  0  0  0  0  0  0999 V2000
   -1.3386    2.4194   -0.9562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4640    1.7158    0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7279    1.2486   -0.3290 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6122    0.5494    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2884   -0.8695    0.7291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2234   -1.3820   -0.1874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142   -1.5299    0.5146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1889   -0.8312   -0.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6300   -1.4457   -1.5442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7475    0.2907    0.1895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3150    0.9032    1.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9688    1.5479    1.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5693   -0.4545    0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8024   -0.5372   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8033   -0.8035    0.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0856    3.0238   -0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6808    3.1229   -1.5190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7463    1.7117   -1.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0551    1.3934   -1.3498 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9471    1.1525    1.4684 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2915   -1.2955    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1330   -0.7386   -1.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5802   -2.3785   -0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1846    1.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3377   -2.6337    0.5847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8140   -0.6611   -2.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5742   -1.9973   -1.3591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8470   -2.1076   -1.9317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5240    0.7407   -0.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0598    1.7100    1.7346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4007    0.1741    2.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2032    1.0058    2.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9815    2.5867    1.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2511   -1.5354   -1.6377 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5885    0.2113   -1.6282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9238   -0.3477   -1.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6906   -0.3660    0.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9144   -1.9076    0.8448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6911   -0.5008    1.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
  5 13  1  0
 13 14  1  0
 13 15  1  0
 12  2  1  0
 13  4  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END

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       5.561   5.854   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.807  -0.981   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.751   4.179   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.758   2.046   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.122   1.804   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.780   3.196   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.587   1.677   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.368   4.335   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.710   2.943   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.395   0.158   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.903   4.462   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.930   0.285   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.175   2.816   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.518   1.424   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.359   2.690   0.000  0.00  0.00           C+0
CONECT    1   11                                                            
CONECT    2   12                                                            
CONECT    3   15                                                            
CONECT    4   15                                                            
CONECT    5    6    7                                                       
CONECT    6    5   11                                                       
CONECT    7    5   12                                                       
CONECT    8    9   11                                                       
CONECT    9    8   13                                                       
CONECT   10   12   14                                                       
CONECT   11    1    6    8                                                  
CONECT   12    2    7   10                                                  
CONECT   13    9   14   15                                                  
CONECT   14   10   13   15                                                  
CONECT   15    3    4   13   14                                             
MASTER        0    0    0    0    0    0    0    0   15    0   32    0
END

COMPND    HMDB0038137
HETATM    1  C1  UNL     1      -1.339   2.419  -0.956  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.464   1.716   0.015  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.728   1.249  -0.329  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.612   0.549   0.612  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.288  -0.870   0.729  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.223  -1.382  -0.187  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.114  -1.530   0.515  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.189  -0.831  -0.246  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.630  -1.446  -1.544  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.747   0.291   0.190  1.00  0.00           C  
HETATM   11  C11 UNL     1      -2.315   0.903   1.474  1.00  0.00           C  
HETATM   12  C12 UNL     1      -0.969   1.548   1.402  1.00  0.00           C  
HETATM   13  C13 UNL     1       2.569  -0.455   0.105  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.802  -0.537  -1.368  1.00  0.00           C  
HETATM   15  C15 UNL     1       3.803  -0.803   0.938  1.00  0.00           C  
HETATM   16  H1  UNL     1      -2.086   3.024  -0.444  1.00  0.00           H  
HETATM   17  H2  UNL     1      -0.681   3.123  -1.519  1.00  0.00           H  
HETATM   18  H3  UNL     1      -1.746   1.712  -1.707  1.00  0.00           H  
HETATM   19  H4  UNL     1       1.055   1.393  -1.350  1.00  0.00           H  
HETATM   20  H5  UNL     1       1.947   1.152   1.468  1.00  0.00           H  
HETATM   21  H6  UNL     1       1.291  -1.295   1.762  1.00  0.00           H  
HETATM   22  H7  UNL     1       0.133  -0.739  -1.086  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.580  -2.378  -0.573  1.00  0.00           H  
HETATM   24  H9  UNL     1      -1.071  -1.185   1.573  1.00  0.00           H  
HETATM   25  H10 UNL     1      -1.338  -2.634   0.585  1.00  0.00           H  
HETATM   26  H11 UNL     1      -2.814  -0.661  -2.310  1.00  0.00           H  
HETATM   27  H12 UNL     1      -3.574  -1.997  -1.359  1.00  0.00           H  
HETATM   28  H13 UNL     1      -1.847  -2.108  -1.932  1.00  0.00           H  
HETATM   29  H14 UNL     1      -3.524   0.741  -0.420  1.00  0.00           H  
HETATM   30  H15 UNL     1      -3.060   1.710   1.735  1.00  0.00           H  
HETATM   31  H16 UNL     1      -2.401   0.174   2.325  1.00  0.00           H  
HETATM   32  H17 UNL     1      -0.203   1.006   2.031  1.00  0.00           H  
HETATM   33  H18 UNL     1      -0.981   2.587   1.847  1.00  0.00           H  
HETATM   34  H19 UNL     1       3.251  -1.535  -1.638  1.00  0.00           H  
HETATM   35  H20 UNL     1       3.588   0.211  -1.628  1.00  0.00           H  
HETATM   36  H21 UNL     1       1.924  -0.348  -1.983  1.00  0.00           H  
HETATM   37  H22 UNL     1       4.691  -0.366   0.441  1.00  0.00           H  
HETATM   38  H23 UNL     1       3.914  -1.908   0.845  1.00  0.00           H  
HETATM   39  H24 UNL     1       3.691  -0.501   1.990  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3    3   12
CONECT    3    4   19
CONECT    4    5   13   20
CONECT    5    6   13   21
CONECT    6    7   22   23
CONECT    7    8   24   25
CONECT    8    9   10   10
CONECT    9   26   27   28
CONECT   10   11   29
CONECT   11   12   30   31
CONECT   12   32   33
CONECT   13   14   15
CONECT   14   34   35   36
CONECT   15   37   38   39
END

HMDB0038137
     RDKit          3D
Bicyclogermacrene
 39 40  0  0  0  0  0  0  0  0999 V2000
   -1.3386    2.4194   -0.9562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4640    1.7158    0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7279    1.2486   -0.3290 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6122    0.5494    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2884   -0.8695    0.7291 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2234   -1.3820   -0.1874 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1142   -1.5299    0.5146 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1889   -0.8312   -0.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6300   -1.4457   -1.5442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7475    0.2907    0.1895 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3150    0.9032    1.4737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9688    1.5479    1.4021 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5693   -0.4545    0.1052 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8024   -0.5372   -1.3682 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8033   -0.8035    0.9383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0856    3.0238   -0.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6808    3.1229   -1.5190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7463    1.7117   -1.7068 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0551    1.3934   -1.3498 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9471    1.1525    1.4684 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2915   -1.2955    1.7615 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1330   -0.7386   -1.0865 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5802   -2.3785   -0.5734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0715   -1.1846    1.5725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3377   -2.6337    0.5847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8140   -0.6611   -2.3097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5742   -1.9973   -1.3591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8470   -2.1076   -1.9317 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5240    0.7407   -0.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0598    1.7100    1.7346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4007    0.1741    2.3254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2032    1.0058    2.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9815    2.5867    1.8467 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2511   -1.5354   -1.6377 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5885    0.2113   -1.6282 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9238   -0.3477   -1.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6906   -0.3660    0.4411 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9144   -1.9076    0.8448 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6911   -0.5008    1.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  2  0
 10 11  1  0
 11 12  1  0
  5 13  1  0
 13 14  1  0
 13 15  1  0
 12  2  1  0
 13  4  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  9 26  1  0
  9 27  1  0
  9 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  0
 12 33  1  0
 14 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 15 38  1  0
 15 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N(6)-(N-Threonylcarbonyl)adenosine	HMDB

Chemical Formula

C₁₅H₂₄

Average Molecular Weight

204.3511

Monoisotopic Molecular Weight

204.187800768

IUPAC Name

(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

Traditional Name

(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene

CAS Registry Number

24703-35-3

SMILES

C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C

InChI Identifier

InChI=1S/C15H24/c1-11-6-5-7-12(2)10-14-13(9-8-11)15(14,3)4/h6,10,13-14H,5,7-9H2,1-4H3/b11-6-,12-10-

InChI Key

VPDZRSSKICPUEY-SUYBHAEQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]Undecane, 9CI) skeleton or the isolepidozane skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Bicyclogermacrane and isolepidozane sesquiterpenoids

Alternative Parents

Substituents

Bicyclogermacrane sesquiterpenoid
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

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0038137)

Source

Endogenous

Endogenous (HMDB: HMDB0038137)

Plant

Plant (HMDB: HMDB0038137)

Animal

Animal (HMDB: HMDB0038137)

Exogenous

Food

Food (HMDB: HMDB0038137)

Citrus (FooDB: FOOD00859)

Exogenous (HMDB: HMDB0038137)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0038137)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0038137)

Lipid metabolism pathway (HMDB: HMDB0038137)

Cellular process

Cell signaling (HMDB: HMDB0038137)

Biochemical process

Lipid transport (HMDB: HMDB0038137)

Role

Biological role

Energy source (HMDB: HMDB0038137)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0038137)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	267.00 to 268.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	0.058 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	6.498 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0084 g/L	ALOGPS
logP	5.09	ALOGPS
logP	4.46	ChemAxon
logS	-4.4	ALOGPS
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	0 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	68.52 m³·mol⁻¹	ChemAxon
Polarizability	25.91 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]+	148.518	31661259
DarkChem	[M-H]-	146.187	31661259
DeepCCS	[M+H]+	158.598	30932474
DeepCCS	[M-H]-	156.24	30932474
DeepCCS	[M-2H]-	189.172	30932474
DeepCCS	[M+Na]+	164.691	30932474
AllCCS	[M+H]+	146.3	32859911
AllCCS	[M+H-H2O]+	142.3	32859911
AllCCS	[M+NH4]+	150.1	32859911
AllCCS	[M+Na]+	151.2	32859911
AllCCS	[M-H]-	156.4	32859911
AllCCS	[M+Na-2H]-	156.9	32859911
AllCCS	[M+HCOO]-	157.5	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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. Predicted by Afia on May 17, 2022.	5.87 minutes	32390414
Predicted by Siyang on May 30, 2022	20.6915 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.49 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2740.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	727.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	267.9 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	423.6 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	346.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	797.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	912.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	115.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1696.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	595.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1491.0 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	626.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	475.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	472.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	711.4 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	8.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Bicyclogermacrene	C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C	1683.9	Standard polar	33892256
Bicyclogermacrene	C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C	1465.3	Standard non polar	33892256
Bicyclogermacrene	C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C	1486.1	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 - Bicyclogermacrene GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-1900000000-df419c5498786a94c8f4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bicyclogermacrene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bicyclogermacrene 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 - Bicyclogermacrene 10V, Positive-QTOF	splash10-0a4i-0290000000-216638dbc9bcc0fef59d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Positive-QTOF	splash10-0a4i-3950000000-79ba6cb8f3b30df6ad42	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Positive-QTOF	splash10-014i-9700000000-3a75cef7802fad80da52	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Negative-QTOF	splash10-0udi-0090000000-9b6e63803a1d9e7a723d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Negative-QTOF	splash10-0udi-0390000000-00526b8f3a27bdd8e099	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Negative-QTOF	splash10-01y9-1900000000-54c856e9a961651a0cfe	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Negative-QTOF	splash10-0udi-0090000000-0b1ac00c3b3c6c0a73b9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Positive-QTOF	splash10-0a4i-0190000000-695c9202804f5c6577ea	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Positive-QTOF	splash10-0a4i-0490000000-8ad2959b26bbbbcf295b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Positive-QTOF	splash10-0006-8900000000-80e416b8aa432948f8ed	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB017365

KNApSAcK ID

C00012425

Chemspider ID

20119973

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Germacrene

METLIN ID

Not Available

PubChem Compound

21159022

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1551871

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 Bicyclogermacrene (HMDB0038137)

MOL for HMDB0038137 (Bicyclogermacrene)

3D MOL for HMDB0038137 (Bicyclogermacrene)

3D SDF for HMDB0038137 (Bicyclogermacrene)

3D-SDF for HMDB0038137 (Bicyclogermacrene)

PDB for HMDB0038137 (Bicyclogermacrene)

3D PDB for HMDB0038137 (Bicyclogermacrene)

SMILES for HMDB0038137 (Bicyclogermacrene)

INCHI for HMDB0038137 (Bicyclogermacrene)

Structure for HMDB0038137 (Bicyclogermacrene)

3D Structure for HMDB0038137 (Bicyclogermacrene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra