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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2021-09-23 16:14:29 UTC

Update Date

2021-09-23 16:14:29 UTC

HMDB ID

HMDB0302240

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Germacrene D

Description

Germacrene d, also known as germacrene d, (s-(e,e))-isomer, is a member of the class of compounds known as germacrane sesquiterpenoids. Germacrane sesquiterpenoids are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. Germacrene d can be found in a number of food items such as peppermint, roman camomile, hyssop, and common walnut, which makes germacrene d a potential biomarker for the consumption of these food products.

Structure

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

HMDB0302240
     RDKit          3D
Germacrene D
 39 39  0  0  0  0  0  0  0  0999 V2000
    1.4627   -3.1359    0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2615   -1.8486    0.3632 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5764   -1.4197    1.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4785   -0.6929    1.7306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3643   -0.0421    0.7602 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8678   -0.9486   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6578   -2.1042    0.2307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8281   -0.1285   -1.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8559    1.2570    0.2026 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414    1.7151    0.8060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4010    2.2001   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0900    3.5712   -0.7964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4342    1.4953   -0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7392    0.1249   -0.1062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8025   -0.8902   -0.6696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9745   -3.4215   -0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1499   -3.9218    0.7827 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0552   -1.8152    2.4967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7920   -0.5055    2.7900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3369    0.2619    1.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1063   -1.3552   -0.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9813   -2.7305   -0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0846   -2.7506    0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5714   -1.7259    0.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4758   -0.0140   -2.2280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8361   -0.5850   -1.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705    0.8952   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6129    2.0818    0.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7128    1.1342   -0.9089 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9634    0.9897    1.4230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1905    2.5698    1.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3419    3.3900   -1.6104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6287    4.1938   -0.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9900    4.0404   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.9497   -1.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7628    0.1427    1.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7962   -0.0850   -0.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0133   -0.4150   -1.2714 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3900   -1.4767   -1.4247 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
  6  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15  2  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  5 20  1  1
  6 21  1  0
  7 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
M  END


  Mrv1652309272007342D          

 15 15  0  0  0  0            999 V2000
    0.0460   -0.6248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5990    0.7146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8685    0.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3836    0.9695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5990   -0.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8504    1.0454    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2083    0.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3836   -0.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0460    1.2289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8504   -0.4412    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6385    1.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1375   -1.4291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3647    1.6904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0633    2.4583    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1805    1.5674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  9  6  1  0  0  0  0
  9  2  2  0  0  0  0
 10  1  1  0  0  0  0
  1  5  2  0  0  0  0
  4  2  1  0  0  0  0
  3  4  1  0  0  0  0
  3  8  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
 10  7  1  0  0  0  0
  4 11  2  0  0  0  0
  1 12  1  0  0  0  0
  6 13  1  6  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302240

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)[C@@H]1CC\C(C)=C\CCC(=C)\C=C\1

> <INCHI_IDENTIFIER>
InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h7-8,10,12,15H,3,5-6,9,11H2,1-2,4H3/b10-8+,14-7+/t15-/m0/s1

> <INCHI_KEY>
GAIBLDCXCZKKJE-RXJOXMPGSA-N

> <FORMULA>
C15H24

> <MOLECULAR_WEIGHT>
204.3511

> <EXACT_MASS>
204.187800768

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
25.859352848562885

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1E,6E,8S)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

> <ALOGPS_LOGP>
5.64

> <JCHEM_LOGP>
4.923184751333333

> <ALOGPS_LOGS>
-4.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
70.54950000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.16e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-germacrene D

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0302240
     RDKit          3D
Germacrene D
 39 39  0  0  0  0  0  0  0  0999 V2000
    1.4627   -3.1359    0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2615   -1.8486    0.3632 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5764   -1.4197    1.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4785   -0.6929    1.7306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3643   -0.0421    0.7602 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8678   -0.9486   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6578   -2.1042    0.2307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8281   -0.1285   -1.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8559    1.2570    0.2026 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414    1.7151    0.8060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4010    2.2001   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0900    3.5712   -0.7964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4342    1.4953   -0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7392    0.1249   -0.1062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8025   -0.8902   -0.6696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9745   -3.4215   -0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1499   -3.9218    0.7827 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0552   -1.8152    2.4967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7920   -0.5055    2.7900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3369    0.2619    1.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1063   -1.3552   -0.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9813   -2.7305   -0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0846   -2.7506    0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5714   -1.7259    0.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4758   -0.0140   -2.2280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8361   -0.5850   -1.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705    0.8952   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6129    2.0818    0.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7128    1.1342   -0.9089 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9634    0.9897    1.4230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1905    2.5698    1.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3419    3.3900   -1.6104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6287    4.1938   -0.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9900    4.0404   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.9497   -1.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7628    0.1427    1.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7962   -0.0850   -0.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0133   -0.4150   -1.2714 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3900   -1.4767   -1.4247 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
  6  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15  2  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  5 20  1  1
  6 21  1  0
  7 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
M  END

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0       0.086  -1.166   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.118   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.488   0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.583   1.810   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.118  -0.206   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.587   1.951   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.255   0.564   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.583  -0.682   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.086   2.294   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.587  -0.824   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.059   3.274   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.257  -2.668   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.547   3.155   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.985   4.589   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.070   2.926   0.000  0.00  0.00           C+0
CONECT    1   10    5   12                                                  
CONECT    2    9    4                                                       
CONECT    3    4    8                                                       
CONECT    4    2    3   11                                                  
CONECT    5    1    8                                                       
CONECT    6    9    7   13                                                  
CONECT    7    6   10                                                       
CONECT    8    3    5                                                       
CONECT    9    6    2                                                       
CONECT   10    1    7                                                       
CONECT   11    4                                                            
CONECT   12    1                                                            
CONECT   13    6   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

COMPND    HMDB0302240
HETATM    1  C1  UNL     1       1.463  -3.136   0.128  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.262  -1.849   0.363  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.576  -1.420   1.559  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.478  -0.693   1.731  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.364  -0.042   0.760  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.868  -0.949  -0.343  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.658  -2.104   0.231  1.00  0.00           C  
HETATM    8  C8  UNL     1      -2.828  -0.129  -1.182  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.856   1.257   0.203  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.441   1.715   0.806  1.00  0.00           C  
HETATM   11  C11 UNL     1       1.401   2.200  -0.245  1.00  0.00           C  
HETATM   12  C12 UNL     1       1.090   3.571  -0.796  1.00  0.00           C  
HETATM   13  C13 UNL     1       2.434   1.495  -0.661  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.739   0.125  -0.106  1.00  0.00           C  
HETATM   15  C15 UNL     1       1.803  -0.890  -0.670  1.00  0.00           C  
HETATM   16  H1  UNL     1       1.975  -3.421  -0.770  1.00  0.00           H  
HETATM   17  H2  UNL     1       1.150  -3.922   0.783  1.00  0.00           H  
HETATM   18  H3  UNL     1       1.055  -1.815   2.497  1.00  0.00           H  
HETATM   19  H4  UNL     1      -0.792  -0.505   2.790  1.00  0.00           H  
HETATM   20  H5  UNL     1      -2.337   0.262   1.290  1.00  0.00           H  
HETATM   21  H6  UNL     1      -1.106  -1.355  -0.999  1.00  0.00           H  
HETATM   22  H7  UNL     1      -2.981  -2.731  -0.644  1.00  0.00           H  
HETATM   23  H8  UNL     1      -2.085  -2.751   0.891  1.00  0.00           H  
HETATM   24  H9  UNL     1      -3.571  -1.726   0.707  1.00  0.00           H  
HETATM   25  H10 UNL     1      -2.476  -0.014  -2.228  1.00  0.00           H  
HETATM   26  H11 UNL     1      -3.836  -0.585  -1.242  1.00  0.00           H  
HETATM   27  H12 UNL     1      -2.970   0.895  -0.789  1.00  0.00           H  
HETATM   28  H13 UNL     1      -1.613   2.082   0.263  1.00  0.00           H  
HETATM   29  H14 UNL     1      -0.713   1.134  -0.909  1.00  0.00           H  
HETATM   30  H15 UNL     1       0.963   0.990   1.423  1.00  0.00           H  
HETATM   31  H16 UNL     1       0.190   2.570   1.505  1.00  0.00           H  
HETATM   32  H17 UNL     1       0.342   3.390  -1.610  1.00  0.00           H  
HETATM   33  H18 UNL     1       0.629   4.194  -0.005  1.00  0.00           H  
HETATM   34  H19 UNL     1       1.990   4.040  -1.222  1.00  0.00           H  
HETATM   35  H20 UNL     1       3.068   1.950  -1.434  1.00  0.00           H  
HETATM   36  H21 UNL     1       2.763   0.143   1.016  1.00  0.00           H  
HETATM   37  H22 UNL     1       3.796  -0.085  -0.391  1.00  0.00           H  
HETATM   38  H23 UNL     1       1.013  -0.415  -1.271  1.00  0.00           H  
HETATM   39  H24 UNL     1       2.390  -1.477  -1.425  1.00  0.00           H  
CONECT    1    2    2   16   17
CONECT    2    3   15
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6    9   20
CONECT    6    7    8   21
CONECT    7   22   23   24
CONECT    8   25   26   27
CONECT    9   10   28   29
CONECT   10   11   30   31
CONECT   11   12   13   13
CONECT   12   32   33   34
CONECT   13   14   35
CONECT   14   15   36   37
CONECT   15   38   39
END

HMDB0302240
     RDKit          3D
Germacrene D
 39 39  0  0  0  0  0  0  0  0999 V2000
    1.4627   -3.1359    0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2615   -1.8486    0.3632 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5764   -1.4197    1.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4785   -0.6929    1.7306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3643   -0.0421    0.7602 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8678   -0.9486   -0.3428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6578   -2.1042    0.2307 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8281   -0.1285   -1.1824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8559    1.2570    0.2026 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414    1.7151    0.8060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4010    2.2001   -0.2454 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0900    3.5712   -0.7964 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4342    1.4953   -0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7392    0.1249   -0.1062 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8025   -0.8902   -0.6696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9745   -3.4215   -0.7698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1499   -3.9218    0.7827 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0552   -1.8152    2.4967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7920   -0.5055    2.7900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3369    0.2619    1.2901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1063   -1.3552   -0.9989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9813   -2.7305   -0.6441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0846   -2.7506    0.8908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5714   -1.7259    0.7069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4758   -0.0140   -2.2280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8361   -0.5850   -1.2419 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705    0.8952   -0.7894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6129    2.0818    0.2625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7128    1.1342   -0.9089 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9634    0.9897    1.4230 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1905    2.5698    1.5050 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3419    3.3900   -1.6104 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6287    4.1938   -0.0053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9900    4.0404   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0677    1.9497   -1.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7628    0.1427    1.0159 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7962   -0.0850   -0.3911 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0133   -0.4150   -1.2714 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3900   -1.4767   -1.4247 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
  6  8  1  0
  5  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  2  0
 13 14  1  0
 14 15  1  0
 15  2  1  0
  1 16  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  5 20  1  1
  6 21  1  0
  7 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 12 32  1  0
 12 33  1  0
 12 34  1  0
 13 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
(1E,6E,8S)-1-Methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene	ChEBI
(1E,6E,8S)-1-Methyl-8-(1-methylethyl)-5-methylidenecyclodeca-1,6-diene	ChEBI
(1E,6E,8S)-8-Isopropyl-1-methyl-5-methylenecyclodeca-1,6-diene	ChEBI
Germacrene D	MeSH
Germacrene D, (S-(e,e))-isomer	MeSH
(-)-Germacrene D	PhytoBank

Chemical Formula

C₁₅H₂₄

Average Molecular Weight

204.3511

Monoisotopic Molecular Weight

204.187800768

IUPAC Name

(1E,6E,8S)-1-methyl-5-methylidene-8-(propan-2-yl)cyclodeca-1,6-diene

Traditional Name

(-)-germacrene D

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1CC\C(C)=C\CCC(=C)\C=C\1

InChI Identifier

InChI=1S/C15H24/c1-12(2)15-10-8-13(3)6-5-7-14(4)9-11-15/h7-8,10,12,15H,3,5-6,9,11H2,1-2,4H3/b10-8+,14-7+/t15-/m0/s1

InChI Key

GAIBLDCXCZKKJE-RXJOXMPGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Branched unsaturated hydrocarbon
Cyclic olefin
Unsaturated aliphatic hydrocarbon
Unsaturated hydrocarbon
Olefin
Hydrocarbon
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

germacrene D (CHEBI:49044 )

Ontology

Not Available

Safflower (FooDB: FOOD00042)

Fruit

Other fruit

Fig (FooDB: FOOD00081)

Tropical fruit

Papaya (FooDB: FOOD00041)

Nut

Common walnut (FooDB: FOOD00094)

Process

Not Available

Role

Industrial application

Agriculture

Pesticide

Insecticide

pesticide (HMDB: HMDB0302240)

Biological role

pheromone (HMDB: HMDB0302240)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	5.64	ALOGPS
logP	4.92	ChemAxon
logS	-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	1	ChemAxon
Refractivity	70.55 m³·mol⁻¹	ChemAxon
Polarizability	25.86 Å³	ChemAxon
Number of Rings	1	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
AllCCS	[M+H]+	146.948	32859911
AllCCS	[M+H-H2O]+	142.813	32859911
AllCCS	[M+Na]+	151.909	32859911
AllCCS	[M+NH4]+	150.799	32859911
AllCCS	[M-H]-	155.517	32859911
AllCCS	[M+Na-2H]-	156.334	32859911
AllCCS	[M+HCOO]-	157.33	32859911
DeepCCS	[M+H]+	158.425	30932474
DeepCCS	[M-H]-	156.067	30932474
DeepCCS	[M-2H]-	189.709	30932474
DeepCCS	[M+Na]+	164.79	30932474

Predicted Kovats Retention Indices

Not Available

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 10V, Positive-QTOF	splash10-0a4i-0290000000-7a1f13236ea184ae5250	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 20V, Positive-QTOF	splash10-0a4i-3950000000-d0bf3ad52f6312cdcd0b	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 40V, Positive-QTOF	splash10-0uy1-8900000000-427ba85bfa2af5673fd8	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 10V, Negative-QTOF	splash10-0udi-0090000000-29fa26cbe8315e311414	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 20V, Negative-QTOF	splash10-0udi-0190000000-16ba9494074fbfa9892c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 40V, Negative-QTOF	splash10-000i-2900000000-60c33cb2f320ce9dab35	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 10V, Positive-QTOF	splash10-0a4i-0190000000-d2a448f88c9f072d85d4	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 20V, Positive-QTOF	splash10-0bt9-0970000000-45ec3c0fe38461068551	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 40V, Positive-QTOF	splash10-0006-9000000000-1721daf5b5a2632b9ef7	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 10V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 20V, Negative-QTOF	splash10-0udi-0090000000-7ccf03fa1149a1e9f55f	2021-10-21	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrene D 40V, Negative-QTOF	splash10-0f79-0930000000-eb84177aa08aada85c30	2021-10-21	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5317570

PDB ID

Not Available

ChEBI ID

49044

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Germacrene D (HMDB0302240)

MOL for HMDB0302240 (Germacrene D)

3D MOL for HMDB0302240 (Germacrene D)

3D SDF for HMDB0302240 (Germacrene D)

3D-SDF for HMDB0302240 (Germacrene D)

PDB for HMDB0302240 (Germacrene D)

3D PDB for HMDB0302240 (Germacrene D)

SMILES for HMDB0302240 (Germacrene D)

INCHI for HMDB0302240 (Germacrene D)

Structure for HMDB0302240 (Germacrene D)

3D Structure for HMDB0302240 (Germacrene D)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

GC-MS Spectra

MS/MS Spectra