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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-12 00:47:09 UTC

Update Date

2022-03-07 02:56:10 UTC

HMDB ID

HMDB0039358

Secondary Accession Numbers

HMDB39358

Metabolite Identification

Common Name

Ginsenoyne D

Description

Ginsenoyne D belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Thus, ginsenoyne D is considered to be a fatty alcohol. Based on a literature review a small amount of articles have been published on Ginsenoyne D.

Structure

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

HMDB0039358
     RDKit          3D
Ginsenoyne D
 45 45  0  0  0  0  0  0  0  0999 V2000
   -7.2800    1.0698   -1.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2913   -0.0725   -1.2495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6986   -0.1887    0.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9646    1.0464    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8122    1.3807   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7909    0.2956   -0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1753   -0.0027    0.9365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1547   -1.1212    0.7330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4900   -1.5220    1.8923 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2582   -0.8413    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2121   -1.7373    0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6193   -1.3064    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7705   -0.9756    0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -0.6106    0.5816 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2997   -0.3170    0.7250 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7189    0.0124    0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3836   -0.9899    1.6316 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3797    0.0365   -0.4667 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7368    1.0647   -1.3511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7816    1.9896   -1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0461    0.7946   -2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7085    1.2041   -0.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5189    0.1012   -2.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8573   -1.0085   -1.4385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0682   -1.0923    0.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5641   -0.3078    0.8341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5712    0.8929    1.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6749    1.8839    0.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2211    1.5370   -1.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3240    2.2954    0.0106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971    0.6200   -1.1273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1822   -0.6643   -0.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7120    0.8775    1.3954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9355   -0.4165    1.6288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5187   -1.9656    0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6186    0.1213    1.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0141   -1.7333   -0.9968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0592   -2.7812    0.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8090    1.0016    1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7768   -1.7730    1.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4611    0.2257   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3075   -0.9833   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9525    0.5713   -1.9419 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5222    1.4883   -2.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3117    1.9004   -0.7688 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 13 14  1  0
 14 15  3  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10  8  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  7 34  1  0
  8 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 16 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  1  0
M  END


  Mrv0541 05061311032D          

 19 19  0  0  0  0            999 V2000
   -4.3164   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2256   -0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5112   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6533   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3677   -0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9388   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0822   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2243   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7967   -0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5099   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7967    0.7441    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0974   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  3  0  0  0  0
 12  9  3  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15  4  1  0  0  0  0
 15 12  1  0  0  0  0
 16 13  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 19 16  1  0  0  0  0
 19 17  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0039358

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC1OC1CC#CC#CC(O)CC

> <INCHI_IDENTIFIER>
InChI=1S/C17H26O2/c1-3-5-6-7-10-13-16-17(19-16)14-11-8-9-12-15(18)4-2/h15-18H,3-7,10,13-14H2,1-2H3

> <INCHI_KEY>
WDZQEROINMBCOK-UHFFFAOYSA-N

> <FORMULA>
C17H26O2

> <MOLECULAR_WEIGHT>
262.3871

> <EXACT_MASS>
262.193280076

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
33.81689265440242

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-(3-heptyloxiran-2-yl)octa-4,6-diyn-3-ol

> <ALOGPS_LOGP>
4.97

> <JCHEM_LOGP>
4.660076908333334

> <ALOGPS_LOGS>
-4.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.669996945182586

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.100275035383167

> <JCHEM_PKA_STRONGEST_BASIC>
-3.192334386483804

> <JCHEM_POLAR_SURFACE_AREA>
32.76

> <JCHEM_REFRACTIVITY>
79.77839999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.32e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
8-(3-heptyloxiran-2-yl)octa-4,6-diyn-3-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0039358
     RDKit          3D
Ginsenoyne D
 45 45  0  0  0  0  0  0  0  0999 V2000
   -7.2800    1.0698   -1.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2913   -0.0725   -1.2495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6986   -0.1887    0.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9646    1.0464    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8122    1.3807   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7909    0.2956   -0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1753   -0.0027    0.9365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1547   -1.1212    0.7330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4900   -1.5220    1.8923 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2582   -0.8413    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2121   -1.7373    0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6193   -1.3064    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7705   -0.9756    0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -0.6106    0.5816 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2997   -0.3170    0.7250 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7189    0.0124    0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3836   -0.9899    1.6316 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3797    0.0365   -0.4667 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7368    1.0647   -1.3511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7816    1.9896   -1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0461    0.7946   -2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7085    1.2041   -0.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5189    0.1012   -2.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8573   -1.0085   -1.4385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0682   -1.0923    0.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5641   -0.3078    0.8341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5712    0.8929    1.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6749    1.8839    0.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2211    1.5370   -1.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3240    2.2954    0.0106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971    0.6200   -1.1273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1822   -0.6643   -0.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7120    0.8775    1.3954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9355   -0.4165    1.6288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5187   -1.9656    0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6186    0.1213    1.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0141   -1.7333   -0.9968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0592   -2.7812    0.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8090    1.0016    1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7768   -1.7730    1.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4611    0.2257   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3075   -0.9833   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9525    0.5713   -1.9419 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5222    1.4883   -2.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3117    1.9004   -0.7688 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 13 14  1  0
 14 15  3  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10  8  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  7 34  1  0
  8 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 16 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  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      -8.057  -4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.488  -0.151   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.724  -3.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.154  -0.921   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.723  -4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.819  -2.461   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.153  -1.691   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.389  -3.231   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.486  -3.231   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.487  -0.921   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.055  -4.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.152  -4.001   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.821  -0.151   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.278  -3.231   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.818  -3.231   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.821   1.389   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.048  -1.897   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2   15                                                       
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6   10                                                       
CONECT    8    9   11                                                       
CONECT    9    8   12                                                       
CONECT   10    7   13                                                       
CONECT   11    8   14                                                       
CONECT   12    9   15                                                       
CONECT   13   10   16                                                       
CONECT   14   11   17                                                       
CONECT   15    4   12   18                                                  
CONECT   16   13   17   19                                                  
CONECT   17   14   16   19                                                  
CONECT   18   15                                                            
CONECT   19   16   17                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

COMPND    HMDB0039358
HETATM    1  C1  UNL     1      -7.280   1.070  -1.337  1.00  0.00           C  
HETATM    2  C2  UNL     1      -6.291  -0.072  -1.250  1.00  0.00           C  
HETATM    3  C3  UNL     1      -5.699  -0.189   0.139  1.00  0.00           C  
HETATM    4  C4  UNL     1      -4.965   1.046   0.564  1.00  0.00           C  
HETATM    5  C5  UNL     1      -3.812   1.381  -0.357  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.791   0.296  -0.424  1.00  0.00           C  
HETATM    7  C7  UNL     1      -2.175  -0.003   0.937  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.155  -1.121   0.733  1.00  0.00           C  
HETATM    9  O1  UNL     1      -0.490  -1.522   1.892  1.00  0.00           O  
HETATM   10  C9  UNL     1       0.258  -0.841   0.804  1.00  0.00           C  
HETATM   11  C10 UNL     1       1.212  -1.737   0.095  1.00  0.00           C  
HETATM   12  C11 UNL     1       2.619  -1.306   0.273  1.00  0.00           C  
HETATM   13  C12 UNL     1       3.771  -0.976   0.416  1.00  0.00           C  
HETATM   14  C13 UNL     1       5.127  -0.611   0.582  1.00  0.00           C  
HETATM   15  C14 UNL     1       6.300  -0.317   0.725  1.00  0.00           C  
HETATM   16  C15 UNL     1       7.719   0.012   0.901  1.00  0.00           C  
HETATM   17  O2  UNL     1       8.384  -0.990   1.632  1.00  0.00           O  
HETATM   18  C16 UNL     1       8.380   0.037  -0.467  1.00  0.00           C  
HETATM   19  C17 UNL     1       7.737   1.065  -1.351  1.00  0.00           C  
HETATM   20  H1  UNL     1      -6.782   1.990  -1.696  1.00  0.00           H  
HETATM   21  H2  UNL     1      -8.046   0.795  -2.092  1.00  0.00           H  
HETATM   22  H3  UNL     1      -7.708   1.204  -0.320  1.00  0.00           H  
HETATM   23  H4  UNL     1      -5.519   0.101  -2.014  1.00  0.00           H  
HETATM   24  H5  UNL     1      -6.857  -1.009  -1.438  1.00  0.00           H  
HETATM   25  H6  UNL     1      -5.068  -1.092   0.216  1.00  0.00           H  
HETATM   26  H7  UNL     1      -6.564  -0.308   0.834  1.00  0.00           H  
HETATM   27  H8  UNL     1      -4.571   0.893   1.568  1.00  0.00           H  
HETATM   28  H9  UNL     1      -5.675   1.884   0.600  1.00  0.00           H  
HETATM   29  H10 UNL     1      -4.221   1.537  -1.363  1.00  0.00           H  
HETATM   30  H11 UNL     1      -3.324   2.295   0.011  1.00  0.00           H  
HETATM   31  H12 UNL     1      -1.997   0.620  -1.127  1.00  0.00           H  
HETATM   32  H13 UNL     1      -3.182  -0.664  -0.807  1.00  0.00           H  
HETATM   33  H14 UNL     1      -1.712   0.877   1.395  1.00  0.00           H  
HETATM   34  H15 UNL     1      -2.936  -0.416   1.629  1.00  0.00           H  
HETATM   35  H16 UNL     1      -1.519  -1.966   0.126  1.00  0.00           H  
HETATM   36  H17 UNL     1       0.619   0.121   1.236  1.00  0.00           H  
HETATM   37  H18 UNL     1       1.014  -1.733  -0.997  1.00  0.00           H  
HETATM   38  H19 UNL     1       1.059  -2.781   0.428  1.00  0.00           H  
HETATM   39  H20 UNL     1       7.809   1.002   1.396  1.00  0.00           H  
HETATM   40  H21 UNL     1       7.777  -1.773   1.617  1.00  0.00           H  
HETATM   41  H22 UNL     1       9.461   0.226  -0.291  1.00  0.00           H  
HETATM   42  H23 UNL     1       8.307  -0.983  -0.880  1.00  0.00           H  
HETATM   43  H24 UNL     1       6.953   0.571  -1.942  1.00  0.00           H  
HETATM   44  H25 UNL     1       8.522   1.488  -2.011  1.00  0.00           H  
HETATM   45  H26 UNL     1       7.312   1.900  -0.769  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3   23   24
CONECT    3    4   25   26
CONECT    4    5   27   28
CONECT    5    6   29   30
CONECT    6    7   31   32
CONECT    7    8   33   34
CONECT    8    9   10   35
CONECT    9   10
CONECT   10   11   36
CONECT   11   12   37   38
CONECT   12   13   13   13
CONECT   13   14
CONECT   14   15   15   15
CONECT   15   16
CONECT   16   17   18   39
CONECT   17   40
CONECT   18   19   41   42
CONECT   19   43   44   45
END

HMDB0039358
     RDKit          3D
Ginsenoyne D
 45 45  0  0  0  0  0  0  0  0999 V2000
   -7.2800    1.0698   -1.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2913   -0.0725   -1.2495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6986   -0.1887    0.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9646    1.0464    0.5641 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8122    1.3807   -0.3567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7909    0.2956   -0.4242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1753   -0.0027    0.9365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1547   -1.1212    0.7330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4900   -1.5220    1.8923 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2582   -0.8413    0.8043 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2121   -1.7373    0.0947 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6193   -1.3064    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7705   -0.9756    0.4165 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1275   -0.6106    0.5816 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2997   -0.3170    0.7250 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7189    0.0124    0.9011 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3836   -0.9899    1.6316 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3797    0.0365   -0.4667 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7368    1.0647   -1.3511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7816    1.9896   -1.6962 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0461    0.7946   -2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7085    1.2041   -0.3199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5189    0.1012   -2.0143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8573   -1.0085   -1.4385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0682   -1.0923    0.2164 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5641   -0.3078    0.8341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5712    0.8929    1.5684 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6749    1.8839    0.5996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2211    1.5370   -1.3627 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3240    2.2954    0.0106 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971    0.6200   -1.1273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1822   -0.6643   -0.8069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7120    0.8775    1.3954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9355   -0.4165    1.6288 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5187   -1.9656    0.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6186    0.1213    1.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0141   -1.7333   -0.9968 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0592   -2.7812    0.4284 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8090    1.0016    1.3961 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7768   -1.7730    1.6172 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4611    0.2257   -0.2910 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3075   -0.9833   -0.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9525    0.5713   -1.9419 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5222    1.4883   -2.0107 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3117    1.9004   -0.7688 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  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
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  3  0
 13 14  1  0
 14 15  3  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 10  8  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  7 34  1  0
  8 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 16 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 19 43  1  0
 19 44  1  0
 19 45  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
8-(3-Heptyloxiranyl)-4,6-octadiyn-3-ol, 9ci	HMDB
9,10-Epoxy-4,6-heptadecadiyn-3-ol	HMDB

Chemical Formula

C₁₇H₂₆O₂

Average Molecular Weight

262.3871

Monoisotopic Molecular Weight

262.193280076

IUPAC Name

8-(3-heptyloxiran-2-yl)octa-4,6-diyn-3-ol

Traditional Name

8-(3-heptyloxiran-2-yl)octa-4,6-diyn-3-ol

CAS Registry Number

139163-36-3

SMILES

CCCCCCCC1OC1CC#CC#CC(O)CC

InChI Identifier

InChI=1S/C17H26O2/c1-3-5-6-7-10-13-16-17(19-16)14-11-8-9-12-15(18)4-2/h15-18H,3-7,10,13-14H2,1-2H3

InChI Key

WDZQEROINMBCOK-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cytoplasm (HMDB: HMDB0039358)
Cell membrane (HMDB: HMDB0039358)

Biofluid or Excreta

Urine (HMDB: HMDB0039358)

Cellular substructure

Extracellular (HMDB: HMDB0039358)
Membrane (HMDB: HMDB0039358)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0039358)

Source

Endogenous

Endogenous (HMDB: HMDB0039358)

Plant

Plant (HMDB: HMDB0039358)

Animal

Animal (HMDB: HMDB0039358)

Exogenous

Food

Food (HMDB: HMDB0039358)

Tea

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid peroxidation (HMDB: HMDB0039358)

Biochemical process

Fatty acid metabolism (HMDB: HMDB0039358)

Cellular process

Cell signaling (HMDB: HMDB0039358)

Biochemical pathway

Lipid metabolism pathway (HMDB: HMDB0039358)

Role

Biological role

Membrane stabilizer (HMDB: HMDB0039358)

Nutrient

Nutrient (HMDB: HMDB0039358)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0039358)

Emulsifier (HMDB: HMDB0039358)

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	5.86 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	0.0083 g/L	ALOGPS
logP	4.97	ALOGPS
logP	4.66	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Acidic)	14.1	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.76 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	79.78 m³·mol⁻¹	ChemAxon
Polarizability	33.82 Å³	ChemAxon
Number of Rings	1	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]+	169.308	31661259
DarkChem	[M-H]-	168.886	31661259
DeepCCS	[M+H]+	161.583	30932474
DeepCCS	[M-H]-	158.293	30932474
DeepCCS	[M-2H]-	194.598	30932474
DeepCCS	[M+Na]+	170.398	30932474
AllCCS	[M+H]+	173.4	32859911
AllCCS	[M+H-H2O]+	170.1	32859911
AllCCS	[M+NH4]+	176.5	32859911
AllCCS	[M+Na]+	177.4	32859911
AllCCS	[M-H]-	173.7	32859911
AllCCS	[M+Na-2H]-	174.7	32859911
AllCCS	[M+HCOO]-	175.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Ginsenoyne D	CCCCCCCC1OC1CC#CC#CC(O)CC	3187.7	Standard polar	33892256
Ginsenoyne D	CCCCCCCC1OC1CC#CC#CC(O)CC	2107.8	Standard non polar	33892256
Ginsenoyne D	CCCCCCCC1OC1CC#CC#CC(O)CC	2184.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Ginsenoyne D,1TMS,isomer #1	CCCCCCCC1OC1CC#CC#CC(CC)O[Si](C)(C)C	2236.6	Semi standard non polar	33892256
Ginsenoyne D,1TBDMS,isomer #1	CCCCCCCC1OC1CC#CC#CC(CC)O[Si](C)(C)C(C)(C)C	2443.9	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 - Ginsenoyne D GC-MS (Non-derivatized) - 70eV, Positive	splash10-001l-9850000000-2d347bdddaddbdffad48	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginsenoyne D GC-MS (1 TMS) - 70eV, Positive	splash10-05bu-9421000000-97ab323472249bd7d447	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Ginsenoyne D 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 - Ginsenoyne D 10V, Positive-QTOF	splash10-03di-0490000000-2fafbe9e32bf9119b408	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 20V, Positive-QTOF	splash10-08fs-5920000000-a71200949ad28cee6442	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 40V, Positive-QTOF	splash10-0k96-9200000000-9cf94a95f0351e4c4e6b	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 10V, Negative-QTOF	splash10-03di-0390000000-1c08b06d71a5ce06767e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 20V, Negative-QTOF	splash10-03di-3970000000-b75da7b18521540df5d5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 40V, Negative-QTOF	splash10-052f-9700000000-9e63dff53b35110c3bd0	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 10V, Negative-QTOF	splash10-03di-0090000000-d0e0e12e04020e6173d4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 20V, Negative-QTOF	splash10-03di-4980000000-d548e0be257df8ed0570	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 40V, Negative-QTOF	splash10-0aou-9310000000-85d9aceaf34317a5d4cf	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 10V, Positive-QTOF	splash10-03dj-2590000000-7bfb88ae5099f9123879	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 20V, Positive-QTOF	splash10-0wmj-9630000000-85801759f81b45ee7339	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Ginsenoyne D 40V, Positive-QTOF	splash10-092c-9500000000-03b61651c988a4edad09	2021-09-22	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

FDB018915

KNApSAcK ID

Not Available

Chemspider ID

4476453

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5317635

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1876511

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 Ginsenoyne D (HMDB0039358)

MOL for HMDB0039358 (Ginsenoyne D)

3D MOL for HMDB0039358 (Ginsenoyne D)

3D SDF for HMDB0039358 (Ginsenoyne D)

3D-SDF for HMDB0039358 (Ginsenoyne D)

PDB for HMDB0039358 (Ginsenoyne D)

3D PDB for HMDB0039358 (Ginsenoyne D)

SMILES for HMDB0039358 (Ginsenoyne D)

INCHI for HMDB0039358 (Ginsenoyne D)

Structure for HMDB0039358 (Ginsenoyne D)

3D Structure for HMDB0039358 (Ginsenoyne D)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra