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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:30:07 UTC

Update Date

2022-03-07 02:52:08 UTC

HMDB ID

HMDB0029388

Secondary Accession Numbers

HMDB29388

Metabolite Identification

Common Name

Cucurbic acid

Description

Cucurbic acid, also known as cucurbate, belongs to the class of organic compounds known as jasmonic acids. These are lipids containing or derived from a jasmonic acid, with a structure characterized by the presence of an alkene chain linked to a 2-(3-oxocyclopentyl)acetic acid moiety. Based on a literature review a small amount of articles have been published on Cucurbic acid.

Structure

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

HMDB0029388
     RDKit          3D
Cucurbic acid
 35 35  0  0  0  0  0  0  0  0999 V2000
    4.9187    1.7421    0.6561 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1507    0.4804    0.4161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7910    0.8092   -0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825    0.4500    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3207    0.8012   -0.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3669   -0.5146   -0.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5280   -1.3262    1.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1635   -0.6831    2.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3770   -2.4879    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2789   -1.8204   -0.5435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7149   -0.4574   -0.8368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5719    0.6739   -0.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9074    0.7066   -0.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7981   -0.0707   -0.5723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1957    1.5889   -1.9862 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9448    1.4476    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891    2.3177   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4568    2.4310    1.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017   -0.0771    1.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7363   -0.1065   -0.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7381    1.3537   -1.0238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7932   -0.0922    1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4263    1.3327   -0.9803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1603    1.4504    0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2837   -1.1279   -0.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4696   -1.7369    1.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0030   -1.1562    2.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7230   -3.2410    0.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9986   -2.8570    1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2152   -2.4507   -1.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3154   -1.8310   -0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5888   -0.3328   -1.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6320    0.6169    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875    1.6162   -0.5413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3773    2.5512   -1.7158 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 11  6  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
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 15 35  1  0
M  END

  Mrv0541 02241211082D          

 15 15  0  0  0  0            999 V2000
    0.2062    1.8962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7007    1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2062    0.5770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4534   -0.1647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2781   -0.4119    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5253   -1.1545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0301   -2.1442    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7726   -1.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8555   -0.9893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1951   -0.4949    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2781    0.3298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177    0.8243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6177    1.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2781    2.1442    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8555    0.2468    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1 13  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3 12  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5 15  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0029388

> <DATABASE_NAME>
hmdb

> <SMILES>
CC\C=C\CC1C(O)CCC1CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+

> <INCHI_KEY>
LYSGIJUGUGJIPS-ONEGZZNKSA-N

> <FORMULA>
C12H20O3

> <MOLECULAR_WEIGHT>
212.2854

> <EXACT_MASS>
212.141244506

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
23.748740551566755

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
2.028796624

> <ALOGPS_LOGS>
-1.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.999427344551062

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.849855366098545

> <JCHEM_PKA_STRONGEST_BASIC>
-1.049451099996372

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
59.4817

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0029388
     RDKit          3D
Cucurbic acid
 35 35  0  0  0  0  0  0  0  0999 V2000
    4.9187    1.7421    0.6561 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1507    0.4804    0.4161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7910    0.8092   -0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825    0.4500    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3207    0.8012   -0.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3669   -0.5146   -0.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5280   -1.3262    1.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1635   -0.6831    2.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3770   -2.4879    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2789   -1.8204   -0.5435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7149   -0.4574   -0.8368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5719    0.6739   -0.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9074    0.7066   -0.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7981   -0.0707   -0.5723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1957    1.5889   -1.9862 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9448    1.4476    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891    2.3177   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4568    2.4310    1.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017   -0.0771    1.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7363   -0.1065   -0.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7381    1.3537   -1.0238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7932   -0.0922    1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4263    1.3327   -0.9803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1603    1.4504    0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2837   -1.1279   -0.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4696   -1.7369    1.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0030   -1.1562    2.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7230   -3.2410    0.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9986   -2.8570    1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2152   -2.4507   -1.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3154   -1.8310   -0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5888   -0.3328   -1.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6320    0.6169    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875    1.6162   -0.5413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3773    2.5512   -1.7158 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 11  6  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
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 15 35  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       0.385   3.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.308   2.308   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.385   1.077   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.846  -0.307   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.386  -0.769   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.847  -2.155   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.923  -4.003   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.309  -3.386   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.464  -1.847   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.231  -0.924   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.386   0.616   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.153   1.539   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.153   3.078   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.386   4.003   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       3.464   0.461   0.000  0.00  0.00           O+0
CONECT    1    2   13                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   15                                                  
CONECT    6    5                                                            
CONECT    7    8                                                            
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12    3   11   13                                                  
CONECT   13    1   12   14                                                  
CONECT   14   13                                                            
CONECT   15    5                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

COMPND    HMDB0029388
HETATM    1  C1  UNL     1       4.919   1.742   0.656  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.151   0.480   0.416  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.791   0.809  -0.102  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.683   0.450   0.540  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.321   0.801  -0.016  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.367  -0.515  -0.235  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.528  -1.326   1.010  1.00  0.00           C  
HETATM    8  O1  UNL     1      -1.164  -0.683   2.040  1.00  0.00           O  
HETATM    9  C8  UNL     1      -1.377  -2.488   0.473  1.00  0.00           C  
HETATM   10  C9  UNL     1      -2.279  -1.820  -0.544  1.00  0.00           C  
HETATM   11  C10 UNL     1      -1.715  -0.457  -0.837  1.00  0.00           C  
HETATM   12  C11 UNL     1      -2.572   0.674  -0.347  1.00  0.00           C  
HETATM   13  C12 UNL     1      -3.907   0.707  -0.967  1.00  0.00           C  
HETATM   14  O2  UNL     1      -4.798  -0.071  -0.572  1.00  0.00           O  
HETATM   15  O3  UNL     1      -4.196   1.589  -1.986  1.00  0.00           O  
HETATM   16  H1  UNL     1       5.945   1.448   1.022  1.00  0.00           H  
HETATM   17  H2  UNL     1       5.089   2.318  -0.281  1.00  0.00           H  
HETATM   18  H3  UNL     1       4.457   2.431   1.372  1.00  0.00           H  
HETATM   19  H4  UNL     1       4.102  -0.077   1.371  1.00  0.00           H  
HETATM   20  H5  UNL     1       4.736  -0.106  -0.350  1.00  0.00           H  
HETATM   21  H6  UNL     1       2.738   1.354  -1.024  1.00  0.00           H  
HETATM   22  H7  UNL     1       1.793  -0.092   1.458  1.00  0.00           H  
HETATM   23  H8  UNL     1       0.426   1.333  -0.980  1.00  0.00           H  
HETATM   24  H9  UNL     1      -0.160   1.450   0.710  1.00  0.00           H  
HETATM   25  H10 UNL     1       0.284  -1.128  -0.926  1.00  0.00           H  
HETATM   26  H11 UNL     1       0.470  -1.737   1.327  1.00  0.00           H  
HETATM   27  H12 UNL     1      -2.003  -1.156   2.267  1.00  0.00           H  
HETATM   28  H13 UNL     1      -0.723  -3.241   0.017  1.00  0.00           H  
HETATM   29  H14 UNL     1      -1.999  -2.857   1.302  1.00  0.00           H  
HETATM   30  H15 UNL     1      -2.215  -2.451  -1.471  1.00  0.00           H  
HETATM   31  H16 UNL     1      -3.315  -1.831  -0.211  1.00  0.00           H  
HETATM   32  H17 UNL     1      -1.589  -0.333  -1.947  1.00  0.00           H  
HETATM   33  H18 UNL     1      -2.632   0.617   0.775  1.00  0.00           H  
HETATM   34  H19 UNL     1      -1.988   1.616  -0.541  1.00  0.00           H  
HETATM   35  H20 UNL     1      -4.377   2.551  -1.716  1.00  0.00           H  
CONECT    1    2   16   17   18
CONECT    2    3   19   20
CONECT    3    4    4   21
CONECT    4    5   22
CONECT    5    6   23   24
CONECT    6    7   11   25
CONECT    7    8    9   26
CONECT    8   27
CONECT    9   10   28   29
CONECT   10   11   30   31
CONECT   11   12   32
CONECT   12   13   33   34
CONECT   13   14   14   15
CONECT   15   35
END

HMDB0029388
     RDKit          3D
Cucurbic acid
 35 35  0  0  0  0  0  0  0  0999 V2000
    4.9187    1.7421    0.6561 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1507    0.4804    0.4161 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7910    0.8092   -0.1017 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825    0.4500    0.5403 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3207    0.8012   -0.0157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3669   -0.5146   -0.2353 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5280   -1.3262    1.0098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1635   -0.6831    2.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3770   -2.4879    0.4735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2789   -1.8204   -0.5435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7149   -0.4574   -0.8368 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5719    0.6739   -0.3473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9074    0.7066   -0.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7981   -0.0707   -0.5723 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1957    1.5889   -1.9862 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9448    1.4476    1.0224 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0891    2.3177   -0.2806 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4568    2.4310    1.3719 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1017   -0.0771    1.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7363   -0.1065   -0.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7381    1.3537   -1.0238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7932   -0.0922    1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4263    1.3327   -0.9803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1603    1.4504    0.7101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2837   -1.1279   -0.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4696   -1.7369    1.3265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0030   -1.1562    2.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7230   -3.2410    0.0169 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9986   -2.8570    1.3020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2152   -2.4507   -1.4709 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3154   -1.8310   -0.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5888   -0.3328   -1.9473 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6320    0.6169    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9875    1.6162   -0.5413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3773    2.5512   -1.7158 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 13 15  1  0
 11  6  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
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  0
  7 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  0
 12 33  1  0
 12 34  1  0
 15 35  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Cucurbate	Generator
(+)-Cucurbic acid	HMDB
(3R,6S,7S)-Cucurbic acid	HMDB
3-Hydroxy-2-(2-pentenyl)cyclopentaneacetic acid	HMDB
2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetate	HMDB
6-Epi-7-isocucurbate	HMDB

Chemical Formula

C₁₂H₂₀O₃

Average Molecular Weight

212.2854

Monoisotopic Molecular Weight

212.141244506

IUPAC Name

2-{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

Traditional Name

{3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl}acetic acid

CAS Registry Number

58240-50-9

SMILES

CC\C=C\CC1C(O)CCC1CC(O)=O

InChI Identifier

InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+

InChI Key

LYSGIJUGUGJIPS-ONEGZZNKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as jasmonic acids. These are lipids containing or derived from a jasmonic acid, with a structure characterized by the presence of an alkene chain linked to a 2-(3-oxocyclopentyl)acetic acid moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Lineolic acids and derivatives

Direct Parent

Jasmonic acids

Alternative Parents

Substituents

Jasmonic acid
Cyclopentanol
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0029388)
Membrane (HMDB: HMDB0029388)

Source

Endogenous

Endogenous (HMDB: HMDB0029388)

Exogenous

Exogenous (HMDB: HMDB0029388)

Food

Fruit

Fruits (FooDB: FOOD00871)

Process

Not Available

Role

Not Available

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	2.29 g/L	ALOGPS
logP	2.86	ALOGPS
logP	2.03	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.85	ChemAxon
pKa (Strongest Basic)	-1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	59.48 m³·mol⁻¹	ChemAxon
Polarizability	23.75 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]+	153.565	31661259
DarkChem	[M-H]-	148.987	31661259
DeepCCS	[M+H]+	148.295	30932474
DeepCCS	[M-H]-	144.468	30932474
DeepCCS	[M-2H]-	181.648	30932474
DeepCCS	[M+Na]+	157.246	30932474
AllCCS	[M+H]+	151.6	32859911
AllCCS	[M+H-H2O]+	147.8	32859911
AllCCS	[M+NH4]+	155.1	32859911
AllCCS	[M+Na]+	156.1	32859911
AllCCS	[M-H]-	153.6	32859911
AllCCS	[M+Na-2H]-	154.4	32859911
AllCCS	[M+HCOO]-	155.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Cucurbic acid	CC\C=C\CC1C(O)CCC1CC(O)=O	3127.4	Standard polar	33892256
Cucurbic acid	CC\C=C\CC1C(O)CCC1CC(O)=O	1683.9	Standard non polar	33892256
Cucurbic acid	CC\C=C\CC1C(O)CCC1CC(O)=O	1772.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Cucurbic acid,1TMS,isomer #1	CC/C=C/CC1C(CC(=O)O)CCC1O[Si](C)(C)C	1858.4	Semi standard non polar	33892256
Cucurbic acid,1TMS,isomer #2	CC/C=C/CC1C(O)CCC1CC(=O)O[Si](C)(C)C	1804.6	Semi standard non polar	33892256
Cucurbic acid,2TMS,isomer #1	CC/C=C/CC1C(CC(=O)O[Si](C)(C)C)CCC1O[Si](C)(C)C	1835.7	Semi standard non polar	33892256
Cucurbic acid,1TBDMS,isomer #1	CC/C=C/CC1C(CC(=O)O)CCC1O[Si](C)(C)C(C)(C)C	2109.4	Semi standard non polar	33892256
Cucurbic acid,1TBDMS,isomer #2	CC/C=C/CC1C(O)CCC1CC(=O)O[Si](C)(C)C(C)(C)C	2041.3	Semi standard non polar	33892256
Cucurbic acid,2TBDMS,isomer #1	CC/C=C/CC1C(CC(=O)O[Si](C)(C)C(C)(C)C)CCC1O[Si](C)(C)C(C)(C)C	2308.3	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 - Cucurbic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-067j-8900000000-ea27b13e19b4ee21ced6	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cucurbic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00tu-9063000000-e789bedc7d15a88a57c8	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Cucurbic acid 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 - Cucurbic acid 10V, Positive-QTOF	splash10-01ot-0920000000-07b359fc963c4a542659	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 20V, Positive-QTOF	splash10-00kb-4900000000-f2960126e9b9762f937b	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 40V, Positive-QTOF	splash10-05mo-9300000000-2ca3989ba6e5f8e244f0	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 10V, Negative-QTOF	splash10-03di-0890000000-94d6315ddd3d710c713e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 20V, Negative-QTOF	splash10-03xv-1940000000-698627f32180dd74aea5	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 40V, Negative-QTOF	splash10-0a4l-9500000000-cdda8faa59c50c68b8bd	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 10V, Negative-QTOF	splash10-0a4i-9020000000-618de50fd9bd6271a13c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 20V, Negative-QTOF	splash10-0a4i-9110000000-6c521c084b87632fe665	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 40V, Negative-QTOF	splash10-0006-9300000000-c0820218f03748f0032c	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 10V, Positive-QTOF	splash10-000b-2910000000-08720212bf033794db2b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 20V, Positive-QTOF	splash10-01qm-6900000000-e4f35fb8a549e339fac2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Cucurbic acid 40V, Positive-QTOF	splash10-0563-9100000000-ebbf067862129722f27e	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	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

FDB011264

KNApSAcK ID

C00000234

Chemspider ID

19015737

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6123064

PDB ID

Not Available

ChEBI ID

Not Available

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

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 Cucurbic acid (HMDB0029388)

MOL for HMDB0029388 (Cucurbic acid)

3D MOL for HMDB0029388 (Cucurbic acid)

3D SDF for HMDB0029388 (Cucurbic acid)

3D-SDF for HMDB0029388 (Cucurbic acid)

PDB for HMDB0029388 (Cucurbic acid)

3D PDB for HMDB0029388 (Cucurbic acid)

SMILES for HMDB0029388 (Cucurbic acid)

INCHI for HMDB0029388 (Cucurbic acid)

Structure for HMDB0029388 (Cucurbic acid)

3D Structure for HMDB0029388 (Cucurbic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra