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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 20:56:00 UTC

Update Date

2022-03-07 02:54:41 UTC

HMDB ID

HMDB0035889

Secondary Accession Numbers

HMDB35889

Metabolite Identification

Common Name

Germacrone 4,5-epoxide

Description

Germacrone 4,5-epoxide 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. Based on a literature review a significant number of articles have been published on Germacrone 4,5-epoxide.

Structure

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

HMDB0035889
     RDKit          3D
Germacrone 4,5-epoxide
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.2954    1.2743    1.1372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7026    0.2182    0.2797 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5819   -0.9264   -0.0680 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.2629   -0.1692 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9219   -0.8344   -1.0298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4383   -2.0227   -0.2638 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0534   -1.8957    1.0699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9313   -2.1845    0.0126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4964   -3.5863    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8889   -1.0605   -0.2476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8706   -0.1297    0.9408 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080    1.2023    0.7153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924    2.1148   -0.0031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5094    3.4462   -0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5179    1.8929   -0.6530 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905    1.3785    0.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8005    1.9752    1.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8489    1.2768    2.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0323    2.2583    0.6541 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3956    1.2238    1.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0943   -1.8840    0.1992 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5451   -0.8991    0.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7632   -0.8681   -1.1576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8066   -1.1202   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862   -0.4502   -1.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -2.9652   -0.4196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4746   -3.9324    1.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9566   -4.2751   -0.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5590   -3.5894   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9234   -1.5236   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7751   -0.5851   -1.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4920   -0.6839    1.7226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8645   -0.1574    1.4571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3871    1.4396    1.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2530    3.3839   -0.9511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9791    3.6603    0.8570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7721    4.2284   -0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199    2.9263   -0.9524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877    1.4112   -1.6601 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
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  4  1  0
  8  6  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  9 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
M  END


  Mrv0541 05061308462D          

 17 18  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9077    2.2982    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6283    1.9049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 O   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
 10  1  1  0  0  0  0
 10  2  1  0  0  0  0
 11  3  1  0  0  0  0
 11  6  2  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  2  0  0  0  0
 13  8  1  0  0  0  0
 13 12  1  0  0  0  0
 14  9  1  0  0  0  0
 15  4  1  0  0  0  0
 15  7  1  0  0  0  0
 15 14  1  0  0  0  0
 16 13  2  0  0  0  0
 17 14  1  0  0  0  0
 17 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0035889

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=C1CC2OC2(C)CC\C=C(C)/CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O2/c1-10(2)12-9-14-15(4,17-14)7-5-6-11(3)8-13(12)16/h6,14H,5,7-9H2,1-4H3/b11-6-

> <INCHI_KEY>
DWGVRYKQVZGSIB-WDZFZDKYSA-N

> <FORMULA>
C15H22O2

> <MOLECULAR_WEIGHT>
234.334

> <EXACT_MASS>
234.161979948

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
26.90396185195299

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6Z)-6,10-dimethyl-3-(propan-2-ylidene)-11-oxabicyclo[8.1.0]undec-6-en-4-one

> <ALOGPS_LOGP>
3.20

> <JCHEM_LOGP>
3.2098705619999994

> <ALOGPS_LOGS>
-3.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.874410558778173

> <JCHEM_PKA_STRONGEST_BASIC>
-4.11727241476301

> <JCHEM_POLAR_SURFACE_AREA>
29.6

> <JCHEM_REFRACTIVITY>
70.5425

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(6Z)-6,10-dimethyl-3-(propan-2-ylidene)-11-oxabicyclo[8.1.0]undec-6-en-4-one

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0035889
     RDKit          3D
Germacrone 4,5-epoxide
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.2954    1.2743    1.1372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7026    0.2182    0.2797 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5819   -0.9264   -0.0680 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.2629   -0.1692 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9219   -0.8344   -1.0298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4383   -2.0227   -0.2638 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0534   -1.8957    1.0699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9313   -2.1845    0.0126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4964   -3.5863    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8889   -1.0605   -0.2476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8706   -0.1297    0.9408 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080    1.2023    0.7153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924    2.1148   -0.0031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5094    3.4462   -0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5179    1.8929   -0.6530 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905    1.3785    0.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8005    1.9752    1.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8489    1.2768    2.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0323    2.2583    0.6541 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3956    1.2238    1.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0943   -1.8840    0.1992 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5451   -0.8991    0.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7632   -0.8681   -1.1576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8066   -1.1202   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862   -0.4502   -1.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -2.9652   -0.4196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4746   -3.9324    1.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9566   -4.2751   -0.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5590   -3.5894   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9234   -1.5236   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7751   -0.5851   -1.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4920   -0.6839    1.7226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8645   -0.1574    1.4571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3871    1.4396    1.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2530    3.3839   -0.9511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9791    3.6603    0.8570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7721    4.2284   -0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199    2.9263   -0.9524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877    1.4112   -1.6601 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
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  4  1  0
  8  6  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  9 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 14 35  1  0
 14 36  1  0
 14 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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.561   4.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.906   3.556   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334   0.770   0.000  0.00  0.00           O+0
CONECT    1   10                                                            
CONECT    2   10                                                            
CONECT    3   11                                                            
CONECT    4   15                                                            
CONECT    5    6    7                                                       
CONECT    6    5   11                                                       
CONECT    7    5   15                                                       
CONECT    8   11   13                                                       
CONECT    9   12   14                                                       
CONECT   10    1    2   12                                                  
CONECT   11    3    6    8                                                  
CONECT   12    9   10   13                                                  
CONECT   13    8   12   16                                                  
CONECT   14    9   15   17                                                  
CONECT   15    4    7   14   17                                             
CONECT   16   13                                                            
CONECT   17   14   15                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

COMPND    HMDB0035889
HETATM    1  C1  UNL     1       3.295   1.274   1.137  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.703   0.218   0.280  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.582  -0.926  -0.068  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.458   0.263  -0.169  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.922  -0.834  -1.030  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.438  -2.023  -0.264  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.053  -1.896   1.070  1.00  0.00           O  
HETATM    8  C7  UNL     1      -0.931  -2.184   0.013  1.00  0.00           C  
HETATM    9  C8  UNL     1      -1.496  -3.586   0.170  1.00  0.00           C  
HETATM   10  C9  UNL     1      -1.889  -1.061  -0.248  1.00  0.00           C  
HETATM   11  C10 UNL     1      -1.871  -0.130   0.941  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.408   1.202   0.715  1.00  0.00           C  
HETATM   13  C12 UNL     1      -1.792   2.115  -0.003  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.509   3.446  -0.125  1.00  0.00           C  
HETATM   15  C14 UNL     1      -0.518   1.893  -0.653  1.00  0.00           C  
HETATM   16  C15 UNL     1       0.590   1.378   0.166  1.00  0.00           C  
HETATM   17  O2  UNL     1       0.800   1.975   1.268  1.00  0.00           O  
HETATM   18  H1  UNL     1       2.849   1.277   2.145  1.00  0.00           H  
HETATM   19  H2  UNL     1       3.032   2.258   0.654  1.00  0.00           H  
HETATM   20  H3  UNL     1       4.396   1.224   1.153  1.00  0.00           H  
HETATM   21  H4  UNL     1       3.094  -1.884   0.199  1.00  0.00           H  
HETATM   22  H5  UNL     1       4.545  -0.899   0.440  1.00  0.00           H  
HETATM   23  H6  UNL     1       3.763  -0.868  -1.158  1.00  0.00           H  
HETATM   24  H7  UNL     1       1.807  -1.120  -1.677  1.00  0.00           H  
HETATM   25  H8  UNL     1       0.186  -0.450  -1.760  1.00  0.00           H  
HETATM   26  H9  UNL     1       1.045  -2.965  -0.420  1.00  0.00           H  
HETATM   27  H10 UNL     1      -1.475  -3.932   1.210  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.957  -4.275  -0.529  1.00  0.00           H  
HETATM   29  H12 UNL     1      -2.559  -3.589  -0.169  1.00  0.00           H  
HETATM   30  H13 UNL     1      -2.923  -1.524  -0.305  1.00  0.00           H  
HETATM   31  H14 UNL     1      -1.775  -0.585  -1.218  1.00  0.00           H  
HETATM   32  H15 UNL     1      -2.492  -0.684   1.723  1.00  0.00           H  
HETATM   33  H16 UNL     1      -0.865  -0.157   1.457  1.00  0.00           H  
HETATM   34  H17 UNL     1      -3.387   1.440   1.181  1.00  0.00           H  
HETATM   35  H18 UNL     1      -3.253   3.384  -0.951  1.00  0.00           H  
HETATM   36  H19 UNL     1      -2.979   3.660   0.857  1.00  0.00           H  
HETATM   37  H20 UNL     1      -1.772   4.228  -0.418  1.00  0.00           H  
HETATM   38  H21 UNL     1      -0.120   2.926  -0.952  1.00  0.00           H  
HETATM   39  H22 UNL     1      -0.588   1.411  -1.660  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3    4    4
CONECT    3   21   22   23
CONECT    4    5   16
CONECT    5    6   24   25
CONECT    6    7    8   26
CONECT    7    8
CONECT    8    9   10
CONECT    9   27   28   29
CONECT   10   11   30   31
CONECT   11   12   32   33
CONECT   12   13   13   34
CONECT   13   14   15
CONECT   14   35   36   37
CONECT   15   16   38   39
CONECT   16   17   17
END

HMDB0035889
     RDKit          3D
Germacrone 4,5-epoxide
 39 40  0  0  0  0  0  0  0  0999 V2000
    3.2954    1.2743    1.1372 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7026    0.2182    0.2797 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5819   -0.9264   -0.0680 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4579    0.2629   -0.1692 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9219   -0.8344   -1.0298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4383   -2.0227   -0.2638 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0534   -1.8957    1.0699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9313   -2.1845    0.0126 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4964   -3.5863    0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8889   -1.0605   -0.2476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8706   -0.1297    0.9408 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4080    1.2023    0.7153 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7924    2.1148   -0.0031 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5094    3.4462   -0.1247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5179    1.8929   -0.6530 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5905    1.3785    0.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8005    1.9752    1.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8489    1.2768    2.1447 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0323    2.2583    0.6541 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3956    1.2238    1.1529 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0943   -1.8840    0.1992 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5451   -0.8991    0.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7632   -0.8681   -1.1576 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8066   -1.1202   -1.6772 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862   -0.4502   -1.7598 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -2.9652   -0.4196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4746   -3.9324    1.2103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9566   -4.2751   -0.5286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5590   -3.5894   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9234   -1.5236   -0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7751   -0.5851   -1.2184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4920   -0.6839    1.7226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8645   -0.1574    1.4571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3871    1.4396    1.1808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2530    3.3839   -0.9511 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9791    3.6603    0.8570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7721    4.2284   -0.4177 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1199    2.9263   -0.9524 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5877    1.4112   -1.6601 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
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  2  0
 16  4  1  0
  8  6  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  5 24  1  0
  5 25  1  0
  6 26  1  0
  9 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 11 33  1  0
 12 34  1  0
 14 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
(+)-Germacrone-4,5-epoxide	HMDB
(4S,5S)-(+)-Germacrone 4,5-epoxide	HMDB

Chemical Formula

C₁₅H₂₂O₂

Average Molecular Weight

234.334

Monoisotopic Molecular Weight

234.161979948

IUPAC Name

(6Z)-6,10-dimethyl-3-(propan-2-ylidene)-11-oxabicyclo[8.1.0]undec-6-en-4-one

Traditional Name

(6Z)-6,10-dimethyl-3-(propan-2-ylidene)-11-oxabicyclo[8.1.0]undec-6-en-4-one

CAS Registry Number

92691-35-5

SMILES

CC(C)=C1CC2OC2(C)CC\C=C(C)/CC1=O

InChI Identifier

InChI=1S/C15H22O2/c1-10(2)12-9-14-15(4,17-14)7-5-6-11(3)8-13(12)16/h6,14H,5,7-9H2,1-4H3/b11-6-

InChI Key

DWGVRYKQVZGSIB-WDZFZDKYSA-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
Cyclic ketone
Ketone
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cytoplasm (HMDB: HMDB0035889)
Cell membrane (HMDB: HMDB0035889)

Cellular substructure

Extracellular (HMDB: HMDB0035889)
Membrane (HMDB: HMDB0035889)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0035889)

Source

Endogenous

Endogenous (HMDB: HMDB0035889)

Plant

Plant (HMDB: HMDB0035889)

Animal

Animal (HMDB: HMDB0035889)

Exogenous

Food

Food (HMDB: HMDB0035889)

Herb and spice

Spice

Turmeric (FooDB: FOOD00068)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid peroxidation (HMDB: HMDB0035889)

Biochemical process

Fatty acid metabolism (HMDB: HMDB0035889)

Cellular process

Cell signaling (HMDB: HMDB0035889)

Biochemical pathway

Lipid metabolism pathway (HMDB: HMDB0035889)

Role

Biological role

Membrane stabilizer (HMDB: HMDB0035889)

Nutrient

Nutrient (HMDB: HMDB0035889)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0035889)

Emulsifier (HMDB: HMDB0035889)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	59 - 60 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	10.65 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.17 g/L	ALOGPS
logP	3.2	ALOGPS
logP	3.21	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	16.87	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	29.6 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	70.54 m³·mol⁻¹	ChemAxon
Polarizability	26.9 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
DeepCCS	[M+H]+	155.943	30932474
DeepCCS	[M-H]-	153.585	30932474
DeepCCS	[M-2H]-	187.245	30932474
DeepCCS	[M+Na]+	162.213	30932474
AllCCS	[M+H]+	155.0	32859911
AllCCS	[M+H-H2O]+	151.2	32859911
AllCCS	[M+NH4]+	158.6	32859911
AllCCS	[M+Na]+	159.6	32859911
AllCCS	[M-H]-	162.4	32859911
AllCCS	[M+Na-2H]-	162.7	32859911
AllCCS	[M+HCOO]-	163.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Germacrone 4,5-epoxide	CC(C)=C1CC2OC2(C)CC\C=C(C)/CC1=O	2478.9	Standard polar	33892256
Germacrone 4,5-epoxide	CC(C)=C1CC2OC2(C)CC\C=C(C)/CC1=O	1731.8	Standard non polar	33892256
Germacrone 4,5-epoxide	CC(C)=C1CC2OC2(C)CC\C=C(C)/CC1=O	1781.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Germacrone 4,5-epoxide,1TMS,isomer #1	CC(C)=C1CC2OC2(C)CC/C=C(/C)C=C1O[Si](C)(C)C	1988.1	Semi standard non polar	33892256
Germacrone 4,5-epoxide,1TMS,isomer #1	CC(C)=C1CC2OC2(C)CC/C=C(/C)C=C1O[Si](C)(C)C	1879.6	Standard non polar	33892256
Germacrone 4,5-epoxide,1TBDMS,isomer #1	CC(C)=C1CC2OC2(C)CC/C=C(/C)C=C1O[Si](C)(C)C(C)(C)C	2166.2	Semi standard non polar	33892256
Germacrone 4,5-epoxide,1TBDMS,isomer #1	CC(C)=C1CC2OC2(C)CC/C=C(/C)C=C1O[Si](C)(C)C(C)(C)C	2025.7	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Germacrone 4,5-epoxide GC-MS (Non-derivatized) - 70eV, Positive	splash10-014i-1090000000-ff820f5735b1bd8eb09a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Germacrone 4,5-epoxide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Germacrone 4,5-epoxide 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 - Germacrone 4,5-epoxide 10V, Positive-QTOF	splash10-000i-0190000000-8112c7c7d7127f969c35	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 20V, Positive-QTOF	splash10-014u-5980000000-f181cf1b9e06fdab9f7c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 40V, Positive-QTOF	splash10-014i-9100000000-7c61c693c9e5c742232a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 10V, Negative-QTOF	splash10-001i-0090000000-57180333367bb7623da7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 20V, Negative-QTOF	splash10-001i-1290000000-394d854ae458c9b3672f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 40V, Negative-QTOF	splash10-066r-9300000000-26264bc4806df4be4167	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 10V, Positive-QTOF	splash10-000i-0090000000-5c60721eec25e22bfcf5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 20V, Positive-QTOF	splash10-014r-0090000000-c110761e65facfc6b6e5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 40V, Positive-QTOF	splash10-00kf-7390000000-947411dfb42f101c53f6	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 10V, Negative-QTOF	splash10-001i-0090000000-9087f47ed0ae51229a17	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 20V, Negative-QTOF	splash10-001i-0090000000-9087f47ed0ae51229a17	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Germacrone 4,5-epoxide 40V, Negative-QTOF	splash10-014j-0390000000-d144bcf46119f1ac6441	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
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

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

13922652

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1852341

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 Germacrone 4,5-epoxide (HMDB0035889)

MOL for HMDB0035889 (Germacrone 4,5-epoxide)

3D MOL for HMDB0035889 (Germacrone 4,5-epoxide)

3D SDF for HMDB0035889 (Germacrone 4,5-epoxide)

3D-SDF for HMDB0035889 (Germacrone 4,5-epoxide)

PDB for HMDB0035889 (Germacrone 4,5-epoxide)

3D PDB for HMDB0035889 (Germacrone 4,5-epoxide)

SMILES for HMDB0035889 (Germacrone 4,5-epoxide)

INCHI for HMDB0035889 (Germacrone 4,5-epoxide)

Structure for HMDB0035889 (Germacrone 4,5-epoxide)

3D Structure for HMDB0035889 (Germacrone 4,5-epoxide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra