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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 22:38:09 UTC

Update Date

2023-02-21 17:25:50 UTC

HMDB ID

HMDB0037390

Secondary Accession Numbers

HMDB37390

Metabolite Identification

Common Name

Tsibulin 1

Description

Tsibulin 1 belongs to the class of organic compounds known as beta-diketones. These are organic compounds containing two keto groups separated by a single carbon atom. Tsibulin 1 has been detected, but not quantified in, several different foods, such as garden onions (Allium cepa), onion-family vegetables, green onion, garden onion (var.), and red onion. This could make tsibulin 1 a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Tsibulin 1.

Structure

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

HMDB0037390
     RDKit          3D
Tsibulin 1
 37 37  0  0  0  0  0  0  0  0999 V2000
    4.8132    0.6250   -0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6775   -0.0213   -0.7737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3987    0.7762   -0.6146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0494    0.8489    0.8397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8542   -0.5316    1.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -1.2769    0.6946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271   -0.5132    0.8378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6685   -1.2631    0.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9106   -0.4303    0.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7506    0.9557   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1560    1.3795   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905    2.4798   -0.2165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9140    0.1919   -0.8479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0887   -0.9519   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3888   -2.1153   -0.5597 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7994    0.3459   -0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7472    1.7474   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    0.3323    1.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9612   -0.0863   -1.8703 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913   -1.0689   -0.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5287    1.7973   -1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5956    0.2919   -1.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1794    1.5136    1.0437 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9395    1.3343    1.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8198   -1.1088    1.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5839   -0.4479    2.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9688   -1.4168   -0.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6838   -2.2730    1.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7273   -0.3874    1.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4163    0.4988    0.3974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4009   -1.3382   -0.9410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8142   -2.2328    0.6029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1248   -0.3815    1.3966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1636    1.6224    0.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2343    0.8444   -1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9557    0.0990   -1.9667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9452    0.1608   -0.4460 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  2  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 10 35  1  0
 13 36  1  0
 13 37  1  0
M  END

  Mrv0541 05061309462D          

 15 15  0  0  0  0            999 V2000
    3.5108   -4.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2253   -3.9080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9398   -4.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6542   -3.9080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3687   -4.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0832   -3.9080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7976   -4.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5121   -3.9080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9803   -3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1198   -5.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2266   -4.3205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5323   -4.5980    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3128   -5.1410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3528   -4.5118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6997   -5.6930    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  8  7  1  0  0  0  0
 11  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  1  0  0  0  0
 14 12  2  0  0  0  0
 15 13  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0037390

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCC1CC(=O)CC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H22O2/c1-2-3-4-5-6-7-8-11-9-12(14)10-13(11)15/h11H,2-10H2,1H3

> <INCHI_KEY>
SKPOJVSKGJMOJV-UHFFFAOYSA-N

> <FORMULA>
C13H22O2

> <MOLECULAR_WEIGHT>
210.3126

> <EXACT_MASS>
210.161979948

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
25.77475680303695

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-octylcyclopentane-1,3-dione

> <ALOGPS_LOGP>
4.01

> <JCHEM_LOGP>
4.031309171666667

> <ALOGPS_LOGS>
-3.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.749713123013496

> <JCHEM_PKA_STRONGEST_BASIC>
-7.230993407800431

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
61.121100000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.21e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-octylcyclopentane-1,3-dione

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0037390
     RDKit          3D
Tsibulin 1
 37 37  0  0  0  0  0  0  0  0999 V2000
    4.8132    0.6250   -0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6775   -0.0213   -0.7737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3987    0.7762   -0.6146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0494    0.8489    0.8397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8542   -0.5316    1.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -1.2769    0.6946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271   -0.5132    0.8378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6685   -1.2631    0.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9106   -0.4303    0.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7506    0.9557   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1560    1.3795   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905    2.4798   -0.2165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9140    0.1919   -0.8479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0887   -0.9519   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3888   -2.1153   -0.5597 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7994    0.3459   -0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7472    1.7474   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    0.3323    1.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9612   -0.0863   -1.8703 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913   -1.0689   -0.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5287    1.7973   -1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5956    0.2919   -1.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1794    1.5136    1.0437 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9395    1.3343    1.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8198   -1.1088    1.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5839   -0.4479    2.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9688   -1.4168   -0.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6838   -2.2730    1.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7273   -0.3874    1.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4163    0.4988    0.3974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4009   -1.3382   -0.9410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8142   -2.2328    0.6029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1248   -0.3815    1.3966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1636    1.6224    0.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2343    0.8444   -1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9557    0.0990   -1.9667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9452    0.1608   -0.4460 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  2  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 10 35  1  0
 13 36  1  0
 13 37  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       6.553  -8.065   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.887  -7.295   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.221  -8.065   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.555  -7.295   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.888  -8.065   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.222  -7.295   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.556  -8.065   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.889  -7.295   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.630  -7.438   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.890  -9.917   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      17.223  -8.065   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      19.660  -8.583   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.384  -9.597   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      21.192  -8.422   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      16.239 -10.627   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7   11                                                       
CONECT    9   11   12                                                       
CONECT   10   12   13                                                       
CONECT   11    8    9   13                                                  
CONECT   12    9   10   14                                                  
CONECT   13   10   11   15                                                  
CONECT   14   12                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

COMPND    HMDB0037390
HETATM    1  C1  UNL     1       4.813   0.625  -0.017  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.678  -0.021  -0.774  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.399   0.776  -0.615  1.00  0.00           C  
HETATM    4  C4  UNL     1       2.049   0.849   0.840  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.854  -0.532   1.400  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.767  -1.277   0.695  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.527  -0.513   0.838  1.00  0.00           C  
HETATM    8  C8  UNL     1      -1.668  -1.263   0.132  1.00  0.00           C  
HETATM    9  C9  UNL     1      -2.911  -0.430   0.327  1.00  0.00           C  
HETATM   10  C10 UNL     1      -2.751   0.956  -0.270  1.00  0.00           C  
HETATM   11  C11 UNL     1      -4.156   1.380  -0.415  1.00  0.00           C  
HETATM   12  O1  UNL     1      -4.591   2.480  -0.217  1.00  0.00           O  
HETATM   13  C12 UNL     1      -4.914   0.192  -0.848  1.00  0.00           C  
HETATM   14  C13 UNL     1      -4.089  -0.952  -0.372  1.00  0.00           C  
HETATM   15  O2  UNL     1      -4.389  -2.115  -0.560  1.00  0.00           O  
HETATM   16  H1  UNL     1       5.799   0.346  -0.476  1.00  0.00           H  
HETATM   17  H2  UNL     1       4.747   1.747  -0.106  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.819   0.332   1.049  1.00  0.00           H  
HETATM   19  H4  UNL     1       3.961  -0.086  -1.870  1.00  0.00           H  
HETATM   20  H5  UNL     1       3.591  -1.069  -0.457  1.00  0.00           H  
HETATM   21  H6  UNL     1       2.529   1.797  -1.062  1.00  0.00           H  
HETATM   22  H7  UNL     1       1.596   0.292  -1.192  1.00  0.00           H  
HETATM   23  H8  UNL     1       1.179   1.514   1.044  1.00  0.00           H  
HETATM   24  H9  UNL     1       2.940   1.334   1.362  1.00  0.00           H  
HETATM   25  H10 UNL     1       2.820  -1.109   1.394  1.00  0.00           H  
HETATM   26  H11 UNL     1       1.584  -0.448   2.486  1.00  0.00           H  
HETATM   27  H12 UNL     1       0.969  -1.417  -0.378  1.00  0.00           H  
HETATM   28  H13 UNL     1       0.684  -2.273   1.203  1.00  0.00           H  
HETATM   29  H14 UNL     1      -0.727  -0.387   1.911  1.00  0.00           H  
HETATM   30  H15 UNL     1      -0.416   0.499   0.397  1.00  0.00           H  
HETATM   31  H16 UNL     1      -1.401  -1.338  -0.941  1.00  0.00           H  
HETATM   32  H17 UNL     1      -1.814  -2.233   0.603  1.00  0.00           H  
HETATM   33  H18 UNL     1      -3.125  -0.381   1.397  1.00  0.00           H  
HETATM   34  H19 UNL     1      -2.164   1.622   0.393  1.00  0.00           H  
HETATM   35  H20 UNL     1      -2.234   0.844  -1.249  1.00  0.00           H  
HETATM   36  H21 UNL     1      -4.956   0.099  -1.967  1.00  0.00           H  
HETATM   37  H22 UNL     1      -5.945   0.161  -0.446  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3   19   20
CONECT    3    4   21   22
CONECT    4    5   23   24
CONECT    5    6   25   26
CONECT    6    7   27   28
CONECT    7    8   29   30
CONECT    8    9   31   32
CONECT    9   10   14   33
CONECT   10   11   34   35
CONECT   11   12   12   13
CONECT   13   14   36   37
CONECT   14   15   15
END

HMDB0037390
     RDKit          3D
Tsibulin 1
 37 37  0  0  0  0  0  0  0  0999 V2000
    4.8132    0.6250   -0.0171 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6775   -0.0213   -0.7737 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3987    0.7762   -0.6146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0494    0.8489    0.8397 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8542   -0.5316    1.3995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -1.2769    0.6946 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5271   -0.5132    0.8378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6685   -1.2631    0.1317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9106   -0.4303    0.3273 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7506    0.9557   -0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1560    1.3795   -0.4149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5905    2.4798   -0.2165 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9140    0.1919   -0.8479 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0887   -0.9519   -0.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3888   -2.1153   -0.5597 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7994    0.3459   -0.4763 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7472    1.7474   -0.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8192    0.3323    1.0491 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9612   -0.0863   -1.8703 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5913   -1.0689   -0.4566 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5287    1.7973   -1.0615 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5956    0.2919   -1.1921 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1794    1.5136    1.0437 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9395    1.3343    1.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8198   -1.1088    1.3938 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5839   -0.4479    2.4855 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9688   -1.4168   -0.3783 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6838   -2.2730    1.2035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7273   -0.3874    1.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4163    0.4988    0.3974 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4009   -1.3382   -0.9410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8142   -2.2328    0.6029 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1248   -0.3815    1.3966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1636    1.6224    0.3928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2343    0.8444   -1.2488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9557    0.0990   -1.9667 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9452    0.1608   -0.4460 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  2  0
 11 13  1  0
 13 14  1  0
 14 15  2  0
 14  9  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  0
  5 26  1  0
  6 27  1  0
  6 28  1  0
  7 29  1  0
  7 30  1  0
  8 31  1  0
  8 32  1  0
  9 33  1  0
 10 34  1  0
 10 35  1  0
 13 36  1  0
 13 37  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
4-Octylcyclopentane-1,3-dione	HMDB

Chemical Formula

C₁₃H₂₂O₂

Average Molecular Weight

210.3126

Monoisotopic Molecular Weight

210.161979948

IUPAC Name

4-octylcyclopentane-1,3-dione

Traditional Name

4-octylcyclopentane-1,3-dione

CAS Registry Number

126624-26-8

SMILES

CCCCCCCCC1CC(=O)CC1=O

InChI Identifier

InChI=1S/C13H22O2/c1-2-3-4-5-6-7-8-11-9-12(14)10-13(11)15/h11H,2-10H2,1H3

InChI Key

SKPOJVSKGJMOJV-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta-diketones. These are organic compounds containing two keto groups separated by a single carbon atom.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Beta-diketones

Alternative Parents

Substituents

1,3-diketone
Cyclic ketone
Ketone
Organic oxide
Hydrocarbon derivative
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0037390)
Cell membrane (HMDB: HMDB0037390)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0037390)

Source

Exogenous

Exogenous (HMDB: HMDB0037390)

Food

Food (HMDB: HMDB0037390)

Herb and spice

Herb

Welsh onion (FooDB: FOOD00241)

Vegetable

Onion-family vegetable

Garden onion (FooDB: FOOD00006)
Garden onion (var.) (FooDB: FOOD00226)
Onion-family vegetables (FooDB: FOOD00855)
Green onion (FooDB: FOOD00963)
Red onion (FooDB: FOOD00962)

Endogenous

Plant

Plant (HMDB: HMDB0037390)

Process

Not Available

Role

Biological role

Nutrient (HMDB: HMDB0037390)

Physical Properties

State

Not Available

Experimental Molecular Properties

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

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.062 g/L	ALOGPS
logP	4.01	ALOGPS
logP	4.03	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	7.75	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	34.14 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	61.12 m³·mol⁻¹	ChemAxon
Polarizability	25.77 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	152.733	31661259
DarkChem	[M-H]-	150.766	31661259
DeepCCS	[M+H]+	152.209	30932474
DeepCCS	[M-H]-	148.182	30932474
DeepCCS	[M-2H]-	185.385	30932474
DeepCCS	[M+Na]+	161.14	30932474
AllCCS	[M+H]+	152.7	32859911
AllCCS	[M+H-H2O]+	149.0	32859911
AllCCS	[M+NH4]+	156.2	32859911
AllCCS	[M+Na]+	157.2	32859911
AllCCS	[M-H]-	157.4	32859911
AllCCS	[M+Na-2H]-	158.2	32859911
AllCCS	[M+HCOO]-	159.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Tsibulin 1	CCCCCCCCC1CC(=O)CC1=O	2483.6	Standard polar	33892256
Tsibulin 1	CCCCCCCCC1CC(=O)CC1=O	1658.3	Standard non polar	33892256
Tsibulin 1	CCCCCCCCC1CC(=O)CC1=O	1731.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Tsibulin 1,1TMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C)CC(=O)C1	1831.9	Semi standard non polar	33892256
Tsibulin 1,1TMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C)CC(=O)C1	1849.6	Standard non polar	33892256
Tsibulin 1,1TMS,isomer #2	CCCCCCCCC1CC(O[Si](C)(C)C)=CC1=O	1851.2	Semi standard non polar	33892256
Tsibulin 1,1TMS,isomer #2	CCCCCCCCC1CC(O[Si](C)(C)C)=CC1=O	1788.5	Standard non polar	33892256
Tsibulin 1,1TMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C)CC1=O	1806.0	Semi standard non polar	33892256
Tsibulin 1,1TMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C)CC1=O	1851.1	Standard non polar	33892256
Tsibulin 1,1TMS,isomer #4	CCCCCCCCC1CC(=O)C=C1O[Si](C)(C)C	1849.1	Semi standard non polar	33892256
Tsibulin 1,1TMS,isomer #4	CCCCCCCCC1CC(=O)C=C1O[Si](C)(C)C	1808.3	Standard non polar	33892256
Tsibulin 1,2TMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C)CC(O[Si](C)(C)C)=C1	1970.5	Semi standard non polar	33892256
Tsibulin 1,2TMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C)CC(O[Si](C)(C)C)=C1	1938.8	Standard non polar	33892256
Tsibulin 1,2TMS,isomer #2	CCCCCCCCC1=C(O[Si](C)(C)C)C=C(O[Si](C)(C)C)C1	1992.1	Semi standard non polar	33892256
Tsibulin 1,2TMS,isomer #2	CCCCCCCCC1=C(O[Si](C)(C)C)C=C(O[Si](C)(C)C)C1	2007.1	Standard non polar	33892256
Tsibulin 1,2TMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C)C=C1O[Si](C)(C)C	1977.6	Semi standard non polar	33892256
Tsibulin 1,2TMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C)C=C1O[Si](C)(C)C	2008.7	Standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)CC(=O)C1	2058.2	Semi standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)CC(=O)C1	2048.7	Standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #2	CCCCCCCCC1CC(O[Si](C)(C)C(C)(C)C)=CC1=O	2100.6	Semi standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #2	CCCCCCCCC1CC(O[Si](C)(C)C(C)(C)C)=CC1=O	2000.8	Standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C(C)(C)C)CC1=O	2023.6	Semi standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C(C)(C)C)CC1=O	2062.8	Standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #4	CCCCCCCCC1CC(=O)C=C1O[Si](C)(C)C(C)(C)C	2104.6	Semi standard non polar	33892256
Tsibulin 1,1TBDMS,isomer #4	CCCCCCCCC1CC(=O)C=C1O[Si](C)(C)C(C)(C)C	1969.6	Standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)CC(O[Si](C)(C)C(C)(C)C)=C1	2419.2	Semi standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #1	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)CC(O[Si](C)(C)C(C)(C)C)=C1	2261.4	Standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #2	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)C=C(O[Si](C)(C)C(C)(C)C)C1	2455.4	Semi standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #2	CCCCCCCCC1=C(O[Si](C)(C)C(C)(C)C)C=C(O[Si](C)(C)C(C)(C)C)C1	2328.3	Standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C(C)(C)C)C=C1O[Si](C)(C)C(C)(C)C	2456.0	Semi standard non polar	33892256
Tsibulin 1,2TBDMS,isomer #3	CCCCCCCCC1C=C(O[Si](C)(C)C(C)(C)C)C=C1O[Si](C)(C)C(C)(C)C	2261.6	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Tsibulin 1 GC-MS (Non-derivatized) - 70eV, Positive	splash10-014j-9300000000-c36db11c62d35f5b1cb2	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Tsibulin 1 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 - Tsibulin 1 10V, Positive-QTOF	splash10-03di-1690000000-66b0a24e412cbf60e464	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 20V, Positive-QTOF	splash10-03di-5920000000-189390b02e316d021152	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 40V, Positive-QTOF	splash10-052f-9100000000-8fd7b4ad6d8099854879	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 10V, Negative-QTOF	splash10-0a4i-0190000000-4d88c16b515dce86e3d9	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 20V, Negative-QTOF	splash10-0a4i-1490000000-ead8162d96a7e0b68055	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 40V, Negative-QTOF	splash10-05my-6900000000-4f3d52f5d6e62bd04ea9	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 10V, Positive-QTOF	splash10-06r6-9620000000-4c309d1fd0bdd1025033	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 20V, Positive-QTOF	splash10-0aou-9300000000-c7507678a154b1e56d78	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 40V, Positive-QTOF	splash10-052f-9000000000-13ebc400c62e1f732900	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 10V, Negative-QTOF	splash10-0a4i-0290000000-14b6c6b81a12f9894a51	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 20V, Negative-QTOF	splash10-0a4l-2980000000-7b3acbda28711dc778a2	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Tsibulin 1 40V, Negative-QTOF	splash10-052f-9700000000-231d5252ffe1c4850577	2021-09-23	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB016432

KNApSAcK ID

C00057001

Chemspider ID

157020

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

180441

PDB ID

Not Available

ChEBI ID

174070

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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

Showing metabocard for Tsibulin 1 (HMDB0037390)

MOL for HMDB0037390 (Tsibulin 1)

3D MOL for HMDB0037390 (Tsibulin 1)

3D SDF for HMDB0037390 (Tsibulin 1)

3D-SDF for HMDB0037390 (Tsibulin 1)

PDB for HMDB0037390 (Tsibulin 1)

3D PDB for HMDB0037390 (Tsibulin 1)

SMILES for HMDB0037390 (Tsibulin 1)

INCHI for HMDB0037390 (Tsibulin 1)

Structure for HMDB0037390 (Tsibulin 1)

3D Structure for HMDB0037390 (Tsibulin 1)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra