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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:56:29 UTC

Update Date

2022-03-07 02:55:03 UTC

HMDB ID

HMDB0036767

Secondary Accession Numbers

HMDB36767

Metabolite Identification

Common Name

Zederone

Description

Zederone 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 Zederone.

Structure

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

HMDB0036767
     RDKit          3D
Zederone
 36 38  0  0  0  0  0  0  0  0999 V2000
   -0.1644    2.2252    1.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7926    1.5934    0.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    1.1152    0.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295    0.4806   -1.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8278   -1.0072   -0.9722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6733   -1.5221   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.3883    1.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1051   -2.7497   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4457   -1.4234   -0.7732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.1794    0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8378   -1.9254    1.1376 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7013   -0.1486   -0.1825 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0659   -0.1764    0.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8978   -1.2812    0.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6065    1.0386   -0.3875 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022    1.7540   -0.8339 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4713    1.0893   -0.7284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1056    1.5589   -1.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0153    3.2961    1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8289    2.2037    2.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8454    1.8056    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5638    1.1986    1.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7957    0.8647   -0.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3170    0.8358   -2.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -1.3466   -0.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6889   -1.4009   -2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0850   -0.6980    1.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6661   -2.3679    1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8730   -1.1142    1.5855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3218   -1.4331   -1.8748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539   -1.3374    0.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3546   -2.2379    0.3880 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9763   -1.1728    1.7134 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6598    1.2986   -0.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3091    0.9527   -1.9487 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1254    2.5995   -1.5111 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
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18  2  1  0
  9  6  1  0
 17 12  2  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  9 30  1  0
 14 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 18 36  1  0
M  END


  Mrv0541 02241218592D          

 18 20  0  0  0  0            999 V2000
   -2.0615    0.8265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0615    0.0006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470   -0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6340    0.0006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6340    0.8265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3470    1.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0803   -0.4123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7934    0.0006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7934    0.8265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0803    1.2382    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5782   -0.2540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0615    0.4137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5782    1.0785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2210    0.1108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6340   -0.8238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9307   -0.9959    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0803   -1.2382    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8343   -1.0386    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
  3 15  1  0  0  0  0
  3 16  1  0  0  0  0
  4  7  1  0  0  0  0
  4 15  1  0  0  0  0
  5  6  2  0  0  0  0
  5 10  1  0  0  0  0
  5 14  1  0  0  0  0
  7  8  1  0  0  0  0
  7 17  2  0  0  0  0
  8  9  2  0  0  0  0
  8 11  1  0  0  0  0
  9 10  1  0  0  0  0
  9 13  1  0  0  0  0
 11 12  2  0  0  0  0
 11 18  1  0  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036767

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=COC2=C1C(=O)C1OC1(C)CC\C=C(C)\C2

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O3/c1-9-5-4-6-15(3)14(18-15)13(16)12-10(2)8-17-11(12)7-9/h5,8,14H,4,6-7H2,1-3H3/b9-5+

> <INCHI_KEY>
CVIVANCKIBYAOP-WEVVVXLNSA-N

> <FORMULA>
C15H18O3

> <MOLECULAR_WEIGHT>
246.3016

> <EXACT_MASS>
246.125594442

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
26.35996180896715

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one

> <ALOGPS_LOGP>
2.70

> <JCHEM_LOGP>
2.8549102296666664

> <ALOGPS_LOGS>
-3.51

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.14060182507373

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5724555056299496

> <JCHEM_POLAR_SURFACE_AREA>
42.74

> <JCHEM_REFRACTIVITY>
69.69720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.59e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0036767
     RDKit          3D
Zederone
 36 38  0  0  0  0  0  0  0  0999 V2000
   -0.1644    2.2252    1.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7926    1.5934    0.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    1.1152    0.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295    0.4806   -1.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8278   -1.0072   -0.9722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6733   -1.5221   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.3883    1.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1051   -2.7497   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4457   -1.4234   -0.7732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.1794    0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8378   -1.9254    1.1376 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7013   -0.1486   -0.1825 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0659   -0.1764    0.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8978   -1.2812    0.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6065    1.0386   -0.3875 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022    1.7540   -0.8339 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4713    1.0893   -0.7284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1056    1.5589   -1.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0153    3.2961    1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8289    2.2037    2.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8454    1.8056    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5638    1.1986    1.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7957    0.8647   -0.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3170    0.8358   -2.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -1.3466   -0.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6889   -1.4009   -2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0850   -0.6980    1.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6661   -2.3679    1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8730   -1.1142    1.5855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3218   -1.4331   -1.8748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539   -1.3374    0.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3546   -2.2379    0.3880 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9763   -1.1728    1.7134 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6598    1.2986   -0.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3091    0.9527   -1.9487 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1254    2.5995   -1.5111 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
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18  2  1  0
  9  6  1  0
 17 12  2  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  9 30  1  0
 14 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 18 36  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      -3.848   1.543   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.848   0.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.514  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.183   0.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.183   1.543   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.514   2.311   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.150  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.481   0.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.481   1.543   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.150   2.311   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.946  -0.474   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.848   0.772   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.946   2.013   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.413   0.207   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.183  -1.538   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -3.604  -1.859   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.150  -2.311   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.424  -1.939   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   15   16                                             
CONECT    4    3    7   15                                                  
CONECT    5    6   10   14                                                  
CONECT    6    1    5                                                       
CONECT    7    4    8   17                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10   13                                                  
CONECT   10    5    9                                                       
CONECT   11    8   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13    9   12                                                       
CONECT   14    5                                                            
CONECT   15    3    4                                                       
CONECT   16    3                                                            
CONECT   17    7                                                            
CONECT   18   11                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

COMPND    HMDB0036767
HETATM    1  C1  UNL     1      -0.164   2.225   1.299  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.793   1.593   0.081  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.010   1.115   0.075  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.730   0.481  -1.040  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.828  -1.007  -0.972  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.673  -1.522  -0.119  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.821  -1.388   1.363  1.00  0.00           C  
HETATM    8  O1  UNL     1      -1.105  -2.750  -0.504  1.00  0.00           O  
HETATM    9  C8  UNL     1      -0.446  -1.423  -0.773  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.716  -1.179   0.096  1.00  0.00           C  
HETATM   11  O2  UNL     1       0.838  -1.925   1.138  1.00  0.00           O  
HETATM   12  C10 UNL     1       1.701  -0.149  -0.182  1.00  0.00           C  
HETATM   13  C11 UNL     1       3.066  -0.176   0.034  1.00  0.00           C  
HETATM   14  C12 UNL     1       3.898  -1.281   0.623  1.00  0.00           C  
HETATM   15  C13 UNL     1       3.607   1.039  -0.387  1.00  0.00           C  
HETATM   16  O3  UNL     1       2.602   1.754  -0.834  1.00  0.00           O  
HETATM   17  C14 UNL     1       1.471   1.089  -0.728  1.00  0.00           C  
HETATM   18  C15 UNL     1       0.106   1.559  -1.126  1.00  0.00           C  
HETATM   19  H1  UNL     1      -0.015   3.296   1.026  1.00  0.00           H  
HETATM   20  H2  UNL     1      -0.829   2.204   2.161  1.00  0.00           H  
HETATM   21  H3  UNL     1       0.845   1.806   1.480  1.00  0.00           H  
HETATM   22  H4  UNL     1      -2.564   1.199   1.028  1.00  0.00           H  
HETATM   23  H5  UNL     1      -3.796   0.865  -0.987  1.00  0.00           H  
HETATM   24  H6  UNL     1      -2.317   0.836  -2.006  1.00  0.00           H  
HETATM   25  H7  UNL     1      -3.787  -1.347  -0.577  1.00  0.00           H  
HETATM   26  H8  UNL     1      -2.689  -1.401  -2.010  1.00  0.00           H  
HETATM   27  H9  UNL     1      -1.085  -0.698   1.830  1.00  0.00           H  
HETATM   28  H10 UNL     1      -1.666  -2.368   1.904  1.00  0.00           H  
HETATM   29  H11 UNL     1      -2.873  -1.114   1.585  1.00  0.00           H  
HETATM   30  H12 UNL     1      -0.322  -1.433  -1.875  1.00  0.00           H  
HETATM   31  H13 UNL     1       4.854  -1.337   0.092  1.00  0.00           H  
HETATM   32  H14 UNL     1       3.355  -2.238   0.388  1.00  0.00           H  
HETATM   33  H15 UNL     1       3.976  -1.173   1.713  1.00  0.00           H  
HETATM   34  H16 UNL     1       4.660   1.299  -0.337  1.00  0.00           H  
HETATM   35  H17 UNL     1      -0.309   0.953  -1.949  1.00  0.00           H  
HETATM   36  H18 UNL     1       0.125   2.600  -1.511  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    3   18
CONECT    3    4   22
CONECT    4    5   23   24
CONECT    5    6   25   26
CONECT    6    7    8    9
CONECT    7   27   28   29
CONECT    8    9
CONECT    9   10   30
CONECT   10   11   11   12
CONECT   12   13   17   17
CONECT   13   14   15   15
CONECT   14   31   32   33
CONECT   15   16   34
CONECT   16   17
CONECT   17   18
CONECT   18   35   36
END

HMDB0036767
     RDKit          3D
Zederone
 36 38  0  0  0  0  0  0  0  0999 V2000
   -0.1644    2.2252    1.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7926    1.5934    0.0809 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0096    1.1152    0.0746 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7295    0.4806   -1.0402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8278   -1.0072   -0.9722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6733   -1.5221   -0.1187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8208   -1.3883    1.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1051   -2.7497   -0.5041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4457   -1.4234   -0.7732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7163   -1.1794    0.0964 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8378   -1.9254    1.1376 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7013   -0.1486   -0.1825 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0659   -0.1764    0.0340 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8978   -1.2812    0.6226 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6065    1.0386   -0.3875 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022    1.7540   -0.8339 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4713    1.0893   -0.7284 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1056    1.5589   -1.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0153    3.2961    1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8289    2.2037    2.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8454    1.8056    1.4800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5638    1.1986    1.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7957    0.8647   -0.9866 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3170    0.8358   -2.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7868   -1.3466   -0.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6889   -1.4009   -2.0096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0850   -0.6980    1.8304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6661   -2.3679    1.9042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8730   -1.1142    1.5855 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3218   -1.4331   -1.8748 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8539   -1.3374    0.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3546   -2.2379    0.3880 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9763   -1.1728    1.7134 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6598    1.2986   -0.3371 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3091    0.9527   -1.9487 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1254    2.5995   -1.5111 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
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18  2  1  0
  9  6  1  0
 17 12  2  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
  7 29  1  0
  9 30  1  0
 14 31  1  0
 14 32  1  0
 14 33  1  0
 15 34  1  0
 18 35  1  0
 18 36  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Cyanidin 3-(6-O-p-coumarylglucoside)	HMDB
Cyanidin 3-(6-p-coumaroylglucoside)	HMDB
Cyanidin 3-O-(6''-p-coumaroyl-glucoside)	HMDB
Zederone	MeSH

Chemical Formula

C₁₅H₁₈O₃

Average Molecular Weight

246.3016

Monoisotopic Molecular Weight

246.125594442

IUPAC Name

(8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one

Traditional Name

(8E)-5,9,14-trimethyl-4,12-dioxatricyclo[9.3.0.0³,⁵]tetradeca-1(11),8,13-trien-2-one

CAS Registry Number

7727-79-9

SMILES

CC1=COC2=C1C(=O)C1OC1(C)CC\C=C(C)\C2

InChI Identifier

InChI=1S/C15H18O3/c1-9-5-4-6-15(3)14(18-15)13(16)12-10(2)8-17-11(12)7-9/h5,8,14H,4,6-7H2,1-3H3/b9-5+

InChI Key

CVIVANCKIBYAOP-WEVVVXLNSA-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
Aryl ketone
Aryl alkyl ketone
Furan
Heteroaromatic compound
Ketone
Organoheterocyclic compound
Ether
Oxirane
Oxacycle
Dialkyl ether
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Source

Endogenous

Endogenous (HMDB: HMDB0036767)

Exogenous

Food

Food (HMDB: HMDB0036767)

Exogenous (HMDB: HMDB0036767)

Process

Naturally occurring process

Biological process

Cellular process

Cell signaling (HMDB: HMDB0036767)

Role

Biological role

Energy source (HMDB: HMDB0036767)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036767)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	153.5 - 154 °C	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
Water Solubility	0.076 g/L	ALOGPS
logP	2.7	ALOGPS
logP	2.85	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	15.14	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	42.74 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	69.7 m³·mol⁻¹	ChemAxon
Polarizability	26.36 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	154.65	31661259
DarkChem	[M-H]-	150.249	31661259
DeepCCS	[M+H]+	162.06	30932474
DeepCCS	[M-H]-	159.702	30932474
DeepCCS	[M-2H]-	192.73	30932474
DeepCCS	[M+Na]+	168.153	30932474
AllCCS	[M+H]+	156.3	32859911
AllCCS	[M+H-H2O]+	152.4	32859911
AllCCS	[M+NH4]+	159.9	32859911
AllCCS	[M+Na]+	160.9	32859911
AllCCS	[M-H]-	163.2	32859911
AllCCS	[M+Na-2H]-	162.9	32859911
AllCCS	[M+HCOO]-	162.7	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.	5.86 minutes	32390414
Predicted by Siyang on May 30, 2022	17.4842 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.06 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2343.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	524.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	212.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	300.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	138.9 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	640.5 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	878.9 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	77.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1467.2 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	496.9 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	1506.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	571.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	400.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	435.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	532.2 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	9.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Zederone	CC1=COC2=C1C(=O)C1OC1(C)CC\C=C(C)\C2	2541.1	Standard polar	33892256
Zederone	CC1=COC2=C1C(=O)C1OC1(C)CC\C=C(C)\C2	1807.3	Standard non polar	33892256
Zederone	CC1=COC2=C1C(=O)C1OC1(C)CC\C=C(C)\C2	2013.3	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 - Zederone GC-MS (Non-derivatized) - 70eV, Positive	splash10-003s-3090000000-3440ed8172a145d43063	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Zederone 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 - Zederone 10V, Positive-QTOF	splash10-0002-0090000000-dfb179f736c51fef9ec3	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 20V, Positive-QTOF	splash10-0002-3290000000-57b0b09eea5a72942747	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 40V, Positive-QTOF	splash10-0006-9000000000-e8c50acf616f80050e2d	2016-08-02	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 10V, Negative-QTOF	splash10-0002-0090000000-5a1ce587affb3e85371d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 20V, Negative-QTOF	splash10-0002-0090000000-84fa1adc596be1c286c4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 40V, Negative-QTOF	splash10-0a5a-7910000000-4ea27ab7f39c5a20d971	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 10V, Positive-QTOF	splash10-0002-0090000000-7216d1413b7714a094f6	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 20V, Positive-QTOF	splash10-002b-0090000000-bc563c15d1b661e0b96f	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 40V, Positive-QTOF	splash10-0002-0090000000-9b61bf21c39cb64de8bf	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 10V, Negative-QTOF	splash10-0002-0090000000-851e47b490f6973ef9e5	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 20V, Negative-QTOF	splash10-0002-0090000000-ed1ef60c1b631f7b92d7	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Zederone 40V, Negative-QTOF	splash10-004l-0090000000-f03d8d8692c0f259ff03	2021-09-23	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

FooDB ID

FDB015708

KNApSAcK ID

C00006800

Chemspider ID

24808209

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Phenylacetaldehyde

METLIN ID

Not Available

PubChem Compound

11492496

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1857061

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Zederone (HMDB0036767)

MOL for HMDB0036767 (Zederone)

3D MOL for HMDB0036767 (Zederone)

3D SDF for HMDB0036767 (Zederone)

3D-SDF for HMDB0036767 (Zederone)

PDB for HMDB0036767 (Zederone)

3D PDB for HMDB0036767 (Zederone)

SMILES for HMDB0036767 (Zederone)

INCHI for HMDB0036767 (Zederone)

Structure for HMDB0036767 (Zederone)

3D Structure for HMDB0036767 (Zederone)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra