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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 20:58:10 UTC

Update Date

2022-03-07 02:54:42 UTC

HMDB ID

HMDB0035921

Secondary Accession Numbers

HMDB35921

Metabolite Identification

Common Name

Limonin

Description

Limonin belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. Based on a literature review a significant number of articles have been published on Limonin.

Structure

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

  Mrv0541 02241218112D          

 34 40  0  0  0  0            999 V2000
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   -1.4527   -1.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7388   -2.1660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262   -1.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0262   -0.9279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7388   -0.5166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6850   -0.5166    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6850    0.3047    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

HMDB0035921
     RDKit          3D
Limonin
 64 70  0  0  0  0  0  0  0  0999 V2000
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M  END

  Mrv0541 02241218112D          

 34 40  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0035921

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1(C)OC2CC(=O)OCC22C1CC(=O)C1(C)C2CCC2(C)C(OC(=O)C3OC123)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H30O8/c1-22(2)15-9-16(27)24(4)14(25(15)12-31-18(28)10-17(25)33-22)5-7-23(3)19(13-6-8-30-11-13)32-21(29)20-26(23,24)34-20/h6,8,11,14-15,17,19-20H,5,7,9-10,12H2,1-4H3

> <INCHI_KEY>
KBDSLGBFQAGHBE-UHFFFAOYSA-N

> <FORMULA>
C26H30O8

> <MOLECULAR_WEIGHT>
470.5116

> <EXACT_MASS>
470.194067936

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
47.85702797281153

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
19-(furan-3-yl)-9,9,13,20-tetramethyl-4,8,15,18-tetraoxahexacyclo[11.9.0.0²,⁷.0²,¹⁰.0¹⁴,¹⁶.0¹⁴,²⁰]docosane-5,12,17-trione

> <ALOGPS_LOGP>
3.47

> <JCHEM_LOGP>
2.4571911409999982

> <ALOGPS_LOGS>
-3.77

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.606840669762278

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1218213499743066

> <JCHEM_POLAR_SURFACE_AREA>
104.57000000000001

> <JCHEM_REFRACTIVITY>
114.71920000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.99e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
limonin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0035921
     RDKit          3D
Limonin
 64 70  0  0  0  0  0  0  0  0999 V2000
   -4.4988    0.7496    1.6145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7941    0.8092    0.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5159    1.8928   -0.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9743   -0.4048   -0.3427 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7360   -1.0643   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8323   -2.0325   -1.5614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4684   -1.2306   -2.6387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1731   -1.8236   -3.4814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2216    0.1330   -2.6171 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0022    0.5579   -2.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7980    0.0661   -0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3226    1.0849    0.3846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7296    0.9334    1.7324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8499   -0.2178    1.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8074   -0.7667    3.0225 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0344   -0.8102    0.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0934   -2.3170    0.9782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3568   -0.2500   -0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4369    1.0348   -0.6451 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8883    0.6887   -0.9032 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3882   -0.2792    0.1253 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7367   -1.5648   -0.5838 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6874    0.2663    0.6969 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5845    0.8494   -0.2909 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7903    2.1993   -0.4780 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7181    2.3159   -1.5129 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0286    1.1059   -1.8993 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3837    0.2023   -1.2063 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2896   -0.8347    1.3973 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4754   -1.4368    2.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0061   -2.2671    3.1307 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0485   -1.0903    2.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6795    0.2547    2.4468 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4554   -0.4612    1.2798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6021    0.6903    1.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4092    1.6784    2.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3004   -0.1737    2.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1355    2.5452    0.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2227    1.4305   -1.2458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7889    2.5663   -1.0205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5838   -1.6092    0.5553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4535   -2.8842   -1.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8082   -2.3515   -1.8340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8651    1.6568   -2.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1910    0.1194   -2.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1596    2.1200   -0.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5668    0.8545    2.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2324    1.9098    2.0124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3415   -2.7915    0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8040   -2.6208    1.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8752   -2.8032    1.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0610   -0.9146   -1.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0502    1.6625   -1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4193    1.6165    0.2993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4354    1.6523   -0.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9335    0.2764   -1.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8895   -2.2161   -0.7917 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1415   -1.2612   -1.5931 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5200   -2.1438   -0.0872 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    0.9843    1.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3674    3.0476    0.0225 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0925    3.2584   -1.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -0.8742   -1.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4439   -1.7177    3.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  1  0
 23 29  1  0
 29 30  1  0
 30 31  2  0
 30 32  1  0
 32 33  1  0
 33 34  1  0
 12  2  1  0
 34 16  1  0
 11  5  1  0
 34 21  1  0
 18 11  1  0
 28 24  2  0
 34 32  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  3 38  1  0
  3 39  1  0
  3 40  1  0
  5 41  1  0
  6 42  1  0
  6 43  1  0
 10 44  1  0
 10 45  1  0
 12 46  1  0
 13 47  1  0
 13 48  1  0
 17 49  1  0
 17 50  1  0
 17 51  1  0
 18 52  1  0
 19 53  1  0
 19 54  1  0
 20 55  1  0
 20 56  1  0
 22 57  1  0
 22 58  1  0
 22 59  1  0
 23 60  1  0
 25 61  1  0
 26 62  1  0
 28 63  1  0
 32 64  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      -2.712  -1.732   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.712  -3.273   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.379  -4.043   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.049  -3.273   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.049  -1.732   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.379  -0.964   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.279  -0.964   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.279   0.569   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.049   1.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.379   0.569   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.606  -1.729   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.931  -0.964   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.931   0.569   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.606   1.331   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.178  -1.254   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.087  -2.502   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -4.178  -3.753   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.567  -0.702   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -1.888   0.805   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -3.356   1.280   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.504   0.245   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -5.267  -4.842   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.780  -5.243   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -3.677   2.787   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.279   2.110   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.606   2.872   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.267  -1.735   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.279  -2.497   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -0.049  -0.191   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.286  -4.043   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.854   3.776   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.379   5.243   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.833   5.243   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.351   3.776   0.000  0.00  0.00           C+0
CONECT    1    2    6   15   18                                             
CONECT    2    1    3   17                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6    7   29                                             
CONECT    6    1    5   10                                                  
CONECT    7    5    8   11   28                                             
CONECT    8    7    9   14   25                                             
CONECT    9    8   10                                                       
CONECT   10    6    9                                                       
CONECT   11    7   12   28                                                  
CONECT   12   11   13   27                                                  
CONECT   13   12   14                                                       
CONECT   14    8   13   26                                                  
CONECT   15    1   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17    2   16   22   23                                             
CONECT   18    1   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   24                                                  
CONECT   21   15   20                                                       
CONECT   22   17                                                            
CONECT   23   17                                                            
CONECT   24   20                                                            
CONECT   25    8                                                            
CONECT   26   14   31   34                                                  
CONECT   27   12                                                            
CONECT   28    7   11                                                       
CONECT   29    5                                                            
CONECT   30    4                                                            
CONECT   31   26   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   26   33                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   80    0
END

COMPND    HMDB0035921
HETATM    1  C1  UNL     1      -4.499   0.750   1.614  1.00  0.00           C  
HETATM    2  C2  UNL     1      -3.794   0.809   0.296  1.00  0.00           C  
HETATM    3  C3  UNL     1      -4.516   1.893  -0.521  1.00  0.00           C  
HETATM    4  O1  UNL     1      -3.974  -0.405  -0.343  1.00  0.00           O  
HETATM    5  C4  UNL     1      -2.736  -1.064  -0.373  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.832  -2.032  -1.561  1.00  0.00           C  
HETATM    7  C6  UNL     1      -3.468  -1.231  -2.639  1.00  0.00           C  
HETATM    8  O2  UNL     1      -4.173  -1.824  -3.481  1.00  0.00           O  
HETATM    9  O3  UNL     1      -3.222   0.133  -2.617  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.002   0.558  -2.038  1.00  0.00           C  
HETATM   11  C8  UNL     1      -1.798   0.066  -0.629  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.323   1.085   0.385  1.00  0.00           C  
HETATM   13  C10 UNL     1      -1.730   0.933   1.732  1.00  0.00           C  
HETATM   14  C11 UNL     1      -0.850  -0.218   1.927  1.00  0.00           C  
HETATM   15  O4  UNL     1      -0.807  -0.767   3.023  1.00  0.00           O  
HETATM   16  C12 UNL     1       0.034  -0.810   0.880  1.00  0.00           C  
HETATM   17  C13 UNL     1      -0.093  -2.317   0.978  1.00  0.00           C  
HETATM   18  C14 UNL     1      -0.357  -0.250  -0.437  1.00  0.00           C  
HETATM   19  C15 UNL     1       0.437   1.035  -0.645  1.00  0.00           C  
HETATM   20  C16 UNL     1       1.888   0.689  -0.903  1.00  0.00           C  
HETATM   21  C17 UNL     1       2.388  -0.279   0.125  1.00  0.00           C  
HETATM   22  C18 UNL     1       2.737  -1.565  -0.584  1.00  0.00           C  
HETATM   23  C19 UNL     1       3.687   0.266   0.697  1.00  0.00           C  
HETATM   24  C20 UNL     1       4.584   0.849  -0.291  1.00  0.00           C  
HETATM   25  C21 UNL     1       4.790   2.199  -0.478  1.00  0.00           C  
HETATM   26  C22 UNL     1       5.718   2.316  -1.513  1.00  0.00           C  
HETATM   27  O5  UNL     1       6.029   1.106  -1.899  1.00  0.00           O  
HETATM   28  C23 UNL     1       5.384   0.202  -1.206  1.00  0.00           C  
HETATM   29  O6  UNL     1       4.290  -0.835   1.397  1.00  0.00           O  
HETATM   30  C24 UNL     1       3.475  -1.437   2.349  1.00  0.00           C  
HETATM   31  O7  UNL     1       4.006  -2.267   3.131  1.00  0.00           O  
HETATM   32  C25 UNL     1       2.048  -1.090   2.409  1.00  0.00           C  
HETATM   33  O8  UNL     1       1.679   0.255   2.447  1.00  0.00           O  
HETATM   34  C26 UNL     1       1.455  -0.461   1.280  1.00  0.00           C  
HETATM   35  H1  UNL     1      -5.602   0.690   1.368  1.00  0.00           H  
HETATM   36  H2  UNL     1      -4.409   1.678   2.218  1.00  0.00           H  
HETATM   37  H3  UNL     1      -4.300  -0.174   2.194  1.00  0.00           H  
HETATM   38  H4  UNL     1      -5.136   2.545   0.129  1.00  0.00           H  
HETATM   39  H5  UNL     1      -5.223   1.430  -1.246  1.00  0.00           H  
HETATM   40  H6  UNL     1      -3.789   2.566  -1.020  1.00  0.00           H  
HETATM   41  H7  UNL     1      -2.584  -1.609   0.555  1.00  0.00           H  
HETATM   42  H8  UNL     1      -3.453  -2.884  -1.240  1.00  0.00           H  
HETATM   43  H9  UNL     1      -1.808  -2.351  -1.834  1.00  0.00           H  
HETATM   44  H10 UNL     1      -1.865   1.657  -2.128  1.00  0.00           H  
HETATM   45  H11 UNL     1      -1.191   0.119  -2.671  1.00  0.00           H  
HETATM   46  H12 UNL     1      -2.160   2.120  -0.029  1.00  0.00           H  
HETATM   47  H13 UNL     1      -2.567   0.854   2.481  1.00  0.00           H  
HETATM   48  H14 UNL     1      -1.232   1.910   2.012  1.00  0.00           H  
HETATM   49  H15 UNL     1      -0.341  -2.792   0.011  1.00  0.00           H  
HETATM   50  H16 UNL     1      -0.804  -2.621   1.796  1.00  0.00           H  
HETATM   51  H17 UNL     1       0.875  -2.803   1.297  1.00  0.00           H  
HETATM   52  H18 UNL     1      -0.061  -0.915  -1.290  1.00  0.00           H  
HETATM   53  H19 UNL     1       0.050   1.662  -1.444  1.00  0.00           H  
HETATM   54  H20 UNL     1       0.419   1.616   0.299  1.00  0.00           H  
HETATM   55  H21 UNL     1       2.435   1.652  -0.923  1.00  0.00           H  
HETATM   56  H22 UNL     1       1.933   0.276  -1.933  1.00  0.00           H  
HETATM   57  H23 UNL     1       1.890  -2.216  -0.792  1.00  0.00           H  
HETATM   58  H24 UNL     1       3.142  -1.261  -1.593  1.00  0.00           H  
HETATM   59  H25 UNL     1       3.520  -2.144  -0.087  1.00  0.00           H  
HETATM   60  H26 UNL     1       3.404   0.984   1.511  1.00  0.00           H  
HETATM   61  H27 UNL     1       4.367   3.048   0.022  1.00  0.00           H  
HETATM   62  H28 UNL     1       6.093   3.258  -1.902  1.00  0.00           H  
HETATM   63  H29 UNL     1       5.496  -0.874  -1.366  1.00  0.00           H  
HETATM   64  H30 UNL     1       1.444  -1.718   3.092  1.00  0.00           H  
CONECT    1    2   35   36   37
CONECT    2    3    4   12
CONECT    3   38   39   40
CONECT    4    5
CONECT    5    6   11   41
CONECT    6    7   42   43
CONECT    7    8    8    9
CONECT    9   10
CONECT   10   11   44   45
CONECT   11   12   18
CONECT   12   13   46
CONECT   13   14   47   48
CONECT   14   15   15   16
CONECT   16   17   18   34
CONECT   17   49   50   51
CONECT   18   19   52
CONECT   19   20   53   54
CONECT   20   21   55   56
CONECT   21   22   23   34
CONECT   22   57   58   59
CONECT   23   24   29   60
CONECT   24   25   28   28
CONECT   25   26   26   61
CONECT   26   27   62
CONECT   27   28
CONECT   28   63
CONECT   29   30
CONECT   30   31   31   32
CONECT   32   33   34   64
CONECT   33   34
END

HMDB0035921
     RDKit          3D
Limonin
 64 70  0  0  0  0  0  0  0  0999 V2000
   -4.4988    0.7496    1.6145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7941    0.8092    0.2961 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5159    1.8928   -0.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9743   -0.4048   -0.3427 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7360   -1.0643   -0.3728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8323   -2.0325   -1.5614 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4684   -1.2306   -2.6387 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1731   -1.8236   -3.4814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2216    0.1330   -2.6171 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0022    0.5579   -2.0380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7980    0.0661   -0.6291 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3226    1.0849    0.3846 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7296    0.9334    1.7324 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8499   -0.2178    1.9270 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8074   -0.7667    3.0225 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0344   -0.8102    0.8800 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0934   -2.3170    0.9782 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3568   -0.2500   -0.4368 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4369    1.0348   -0.6451 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8883    0.6887   -0.9032 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3882   -0.2792    0.1253 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7367   -1.5648   -0.5838 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6874    0.2663    0.6969 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5845    0.8494   -0.2909 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7903    2.1993   -0.4780 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7181    2.3159   -1.5129 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0286    1.1059   -1.8993 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3837    0.2023   -1.2063 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2896   -0.8347    1.3973 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4754   -1.4368    2.3487 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0061   -2.2671    3.1307 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0485   -1.0903    2.4090 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6795    0.2547    2.4468 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4554   -0.4612    1.2798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6021    0.6903    1.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4092    1.6784    2.2176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3004   -0.1737    2.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1355    2.5452    0.1289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2227    1.4305   -1.2458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7889    2.5663   -1.0205 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5838   -1.6092    0.5553 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4535   -2.8842   -1.2403 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8082   -2.3515   -1.8340 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8651    1.6568   -2.1276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1910    0.1194   -2.6706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1596    2.1200   -0.0289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5668    0.8545    2.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2324    1.9098    2.0124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3415   -2.7915    0.0113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8040   -2.6208    1.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8752   -2.8032    1.2967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0610   -0.9146   -1.2896 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0502    1.6625   -1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4193    1.6165    0.2993 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4354    1.6523   -0.9225 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9335    0.2764   -1.9331 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8895   -2.2161   -0.7917 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1415   -1.2612   -1.5931 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5200   -2.1438   -0.0872 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    0.9843    1.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3674    3.0476    0.0225 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0925    3.2584   -1.9019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4957   -0.8742   -1.3661 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4439   -1.7177    3.0923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  1  0
 23 29  1  0
 29 30  1  0
 30 31  2  0
 30 32  1  0
 32 33  1  0
 33 34  1  0
 12  2  1  0
 34 16  1  0
 11  5  1  0
 34 21  1  0
 18 11  1  0
 28 24  2  0
 34 32  1  0
  1 35  1  0
  1 36  1  0
  1 37  1  0
  3 38  1  0
  3 39  1  0
  3 40  1  0
  5 41  1  0
  6 42  1  0
  6 43  1  0
 10 44  1  0
 10 45  1  0
 12 46  1  0
 13 47  1  0
 13 48  1  0
 17 49  1  0
 17 50  1  0
 17 51  1  0
 18 52  1  0
 19 53  1  0
 19 54  1  0
 20 55  1  0
 20 56  1  0
 22 57  1  0
 22 58  1  0
 22 59  1  0
 23 60  1  0
 25 61  1  0
 26 62  1  0
 28 63  1  0
 32 64  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
7,16-dioxo-7,16-Dideoxylimondiol	HMDB
Citrolimonin	HMDB
Dictamnolactone	HMDB
Evodia fruit	HMDB
Evodia fruit (JP15)	HMDB
Evodin	HMDB
Evodine?	HMDB
Limone?	HMDB
Limonoate D-ring-lactone	HMDB
Limonoic acid 3,19:16,17-dilactone	HMDB
Limonoic acid, di-delta-lactone	HMDB
Obaculactone	HMDB

Chemical Formula

C₂₆H₃₀O₈

Average Molecular Weight

470.5116

Monoisotopic Molecular Weight

470.194067936

IUPAC Name

19-(furan-3-yl)-9,9,13,20-tetramethyl-4,8,15,18-tetraoxahexacyclo[11.9.0.0²,⁷.0²,¹⁰.0¹⁴,¹⁶.0¹⁴,²⁰]docosane-5,12,17-trione

Traditional Name

limonin

CAS Registry Number

1180-71-8

SMILES

CC1(C)OC2CC(=O)OCC22C1CC(=O)C1(C)C2CCC2(C)C(OC(=O)C3OC123)C1=COC=C1

InChI Identifier

InChI=1S/C26H30O8/c1-22(2)15-9-16(27)24(4)14(25(15)12-31-18(28)10-17(25)33-22)5-7-23(3)19(13-6-8-30-11-13)32-21(29)20-26(23,24)34-20/h6,8,11,14-15,17,19-20H,5,7,9-10,12H2,1-4H3

InChI Key

KBDSLGBFQAGHBE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Limonoid skeleton
Steroid lactone
11-oxosteroid
Oxosteroid
2-oxosteroid
Steroid
Naphthopyran
Naphthalene
Delta valerolactone
Dioxepane
1,4-dioxepane
Delta_valerolactone
Pyran
Oxane
Dicarboxylic acid or derivatives
Tetrahydrofuran
Heteroaromatic compound
Furan
Carboxylic acid ester
Lactone
Ketone
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Dialkyl ether
Oxirane
Ether
Organooxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

a small molecule (LIMONIN )

Ontology

Physiological effect

Organoleptic effect

Taste

Bitter

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0035921)

Source

Endogenous

Endogenous (HMDB: HMDB0035921)

Plant

Plant (HMDB: HMDB0035921)

Animal

Animal (HMDB: HMDB0035921)

Exogenous

Food

Food (HMDB: HMDB0035921)

Fruit

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Sweet orange (FooDB: FOOD00057)
Mandarin orange (Clementine, Tangerine) (FooDB: FOOD00056)
Citrus (FooDB: FOOD00859)
Sour orange (FooDB: FOOD00918)

Exogenous (HMDB: HMDB0035921)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0035921)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0035921)

Lipid metabolism pathway (HMDB: HMDB0035921)

Cellular process

Cell signaling (HMDB: HMDB0035921)

Biochemical process

Lipid transport (HMDB: HMDB0035921)

Role

Biological role

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0035921)

Agriculture

Pesticide (HMDB: HMDB0035921)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	298 °C	Not Available
Boiling Point	668.36 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	270.2 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	0.474 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.08 g/L	ALOGPS
logP	3.47	ALOGPS
logP	2.46	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	17.61	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	104.57 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	114.72 m³·mol⁻¹	ChemAxon
Polarizability	47.86 Å³	ChemAxon
Number of Rings	7	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]+	205.612	31661259
DarkChem	[M-H]-	199.323	31661259
DeepCCS	[M-2H]-	238.806	30932474
DeepCCS	[M+Na]+	214.23	30932474
AllCCS	[M+H]+	208.5	32859911
AllCCS	[M+H-H2O]+	206.5	32859911
AllCCS	[M+NH4]+	210.3	32859911
AllCCS	[M+Na]+	210.8	32859911
AllCCS	[M-H]-	213.3	32859911
AllCCS	[M+Na-2H]-	214.2	32859911
AllCCS	[M+HCOO]-	215.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Limonin	CC1(C)OC2CC(=O)OCC22C1CC(=O)C1(C)C2CCC2(C)C(OC(=O)C3OC123)C1=COC=C1	4328.3	Standard polar	33892256
Limonin	CC1(C)OC2CC(=O)OCC22C1CC(=O)C1(C)C2CCC2(C)C(OC(=O)C3OC123)C1=COC=C1	3158.9	Standard non polar	33892256
Limonin	CC1(C)OC2CC(=O)OCC22C1CC(=O)C1(C)C2CCC2(C)C(OC(=O)C3OC123)C1=COC=C1	4214.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Limonin,1TMS,isomer #1	CC1(C)OC2CC(=O)OCC23C1C=C(O[Si](C)(C)C)C1(C)C3CCC2(C)C(C3=COC=C3)OC(=O)C3OC321	3580.7	Semi standard non polar	33892256
Limonin,1TMS,isomer #1	CC1(C)OC2CC(=O)OCC23C1C=C(O[Si](C)(C)C)C1(C)C3CCC2(C)C(C3=COC=C3)OC(=O)C3OC321	3352.9	Standard non polar	33892256
Limonin,1TBDMS,isomer #1	CC1(C)OC2CC(=O)OCC23C1C=C(O[Si](C)(C)C(C)(C)C)C1(C)C3CCC2(C)C(C3=COC=C3)OC(=O)C3OC321	3818.5	Semi standard non polar	33892256
Limonin,1TBDMS,isomer #1	CC1(C)OC2CC(=O)OCC23C1C=C(O[Si](C)(C)C(C)(C)C)C1(C)C3CCC2(C)C(C3=COC=C3)OC(=O)C3OC321	3577.1	Standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Limonin GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-7091800000-d189c180a34aeb636eb4	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Limonin 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 - Limonin 10V, Positive-QTOF	splash10-0fk9-0000900000-a4ab208d1fffee15d3df	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 20V, Positive-QTOF	splash10-0imr-0012900000-ed371143180c1aea6bc7	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 40V, Positive-QTOF	splash10-000t-9120100000-66524d5b327a652ced01	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 10V, Negative-QTOF	splash10-00or-0000900000-75a3d9f8a0f1fae14750	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 20V, Negative-QTOF	splash10-0g2c-1002900000-4048ea92e5c743c331ac	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 40V, Negative-QTOF	splash10-0002-4009200000-94a0f7fc00188c6b3e35	2017-09-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 10V, Negative-QTOF	splash10-004i-0000900000-d297686d7426b68c96ce	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 20V, Negative-QTOF	splash10-014i-0000900000-ff496abcb051f215a95e	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 40V, Negative-QTOF	splash10-014i-0001900000-52252c8a0c93946623bb	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 10V, Positive-QTOF	splash10-00di-0000900000-b8ab25ad98350c2823ca	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 20V, Positive-QTOF	splash10-00fr-0010900000-f78ec9bfcbf614a341cb	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Limonin 40V, Positive-QTOF	splash10-03gi-1460900000-329d430a9185fb234de4	2021-09-24	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Limonin

METLIN ID

Not Available

PubChem Compound

235284

PDB ID

Not Available

ChEBI ID

16226

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1667071

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

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General References

Matsuda H, Yoshikawa M, Iinuma M, Kubo M: Antinociceptive and anti-inflammatory activities of limonin isolated from the fruits of Evodia rutaecarpa var. bodinieri. Planta Med. 1998 May;64(4):339-42. [PubMed:9619117 ]
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 Limonin (HMDB0035921)

MOL for HMDB0035921 (Limonin)

3D MOL for HMDB0035921 (Limonin)

3D SDF for HMDB0035921 (Limonin)

3D-SDF for HMDB0035921 (Limonin)

PDB for HMDB0035921 (Limonin)

3D PDB for HMDB0035921 (Limonin)

SMILES for HMDB0035921 (Limonin)

INCHI for HMDB0035921 (Limonin)

Structure for HMDB0035921 (Limonin)

3D Structure for HMDB0035921 (Limonin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra