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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 16:31:05 UTC

Update Date

2021-09-26 23:11:41 UTC

HMDB ID

HMDB0256194

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Pedunculagin

Description

Pedunculagin belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. Pedunculagin is found, on average, in the highest concentration within pomegranates (Punica granatum). Pedunculagin has also been detected, but not quantified in, several different foods, such as red tea, walnuts (Juglans), green tea, acorns (Quercus), and red raspberries (Rubus idaeus). This could make pedunculagin a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on Pedunculagin. This compound has been identified in human blood as reported by (PMID: 31557052 ). Pedunculagin is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Pedunculagin is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

  Mrv0541 02241218322D          

 56 62  0  0  0  0            999 V2000
    3.4006   -2.5616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6499   -2.2523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

HMDB0256194
     RDKit          3D
Pedunculagin
 80 86  0  0  0  0  0  0  0  0999 V2000
    1.8693    0.0706   -3.6862 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5683   -0.0625   -2.6082 C   0  0  0  0  0  0  0  0  0  0  0  0
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 56 80  1  0
M  END

  Mrv0541 02241218322D          

 56 62  0  0  0  0            999 V2000
    3.4006   -2.5616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6499   -2.2523    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0256194

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12

> <INCHI_IDENTIFIER>
InChI=1S/C34H24O22/c35-10-1-6-15(23(43)19(10)39)16-7(2-11(36)20(40)24(16)44)31(48)54-27-14(5-52-30(6)47)53-34(51)29-28(27)55-32(49)8-3-12(37)21(41)25(45)17(8)18-9(33(50)56-29)4-13(38)22(42)26(18)46/h1-4,14,27-29,34-46,51H,5H2

> <INCHI_KEY>
IYMHVUYNBVWXKH-UHFFFAOYSA-N

> <FORMULA>
C34H24O22

> <MOLECULAR_WEIGHT>
784.5412

> <EXACT_MASS>
784.075922452

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
69.10001971056522

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
7,8,9,12,13,14,20,28,29,30,33,34,35-tridecahydroxy-3,18,21,24,39-pentaoxaheptacyclo[20.17.0.0²,¹⁹.0⁵,¹⁰.0¹¹,¹⁶.0²⁶,³¹.0³²,³⁷]nonatriaconta-5,7,9,11,13,15,26(31),27,29,32(37),33,35-dodecaene-4,17,25,38-tetrone

> <ALOGPS_LOGP>
2.48

> <JCHEM_LOGP>
1.9538354086666665

> <ALOGPS_LOGS>
-2.45

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.689216480205492

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.250788791154902

> <JCHEM_PKA_STRONGEST_BASIC>
-6.173381888389522

> <JCHEM_POLAR_SURFACE_AREA>
377.42

> <JCHEM_REFRACTIVITY>
177.13860000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.79e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7,8,9,12,13,14,20,28,29,30,33,34,35-tridecahydroxy-3,18,21,24,39-pentaoxaheptacyclo[20.17.0.0²,¹⁹.0⁵,¹⁰.0¹¹,¹⁶.0²⁶,³¹.0³²,³⁷]nonatriaconta-5,7,9,11,13,15,26(31),27,29,32(37),33,35-dodecaene-4,17,25,38-tetrone

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0256194
     RDKit          3D
Pedunculagin
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 41 43  2  0
 43 44  1  0
 43 45  1  0
 45 46  1  0
 45 47  2  0
 47 48  1  0
 48 49  2  0
 49 50  1  0
 50 51  2  0
 51 52  1  0
 51 53  1  0
 53 54  1  0
 53 55  2  0
 55 56  1  0
 49  2  1  0
 35  5  1  0
 47 39  1  0
 55 48  1  0
 34  9  1  0
 21 13  1  0
 29 22  1  0
  4 57  1  0
  4 58  1  0
  5 59  1  0
  7 60  1  0
  8 61  1  0
  9 62  1  0
 14 63  1  0
 16 64  1  0
 18 65  1  0
 20 66  1  0
 24 67  1  0
 26 68  1  0
 28 69  1  0
 30 70  1  0
 34 71  1  0
 35 72  1  0
 40 73  1  0
 42 74  1  0
 44 75  1  0
 46 76  1  0
 50 77  1  0
 52 78  1  0
 54 79  1  0
 56 80  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  O   UNK     0       6.348  -4.782   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.946  -4.204   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.875  -5.358   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.864  -6.513   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.452  -7.996   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.441  -9.068   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.946  -2.802   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.452  -1.566   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.710  -0.329   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.616   0.907   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.039   2.309   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.946   3.545   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -0.247  -8.079   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.166  -6.347   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.401  -6.513   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.143  -7.832   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.555  -9.728   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.968  -8.244   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.979  -7.089   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.391  -5.605   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.989  -4.946   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.166  -3.792   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.401  -3.957   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.225  -5.276   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -3.709  -5.276   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       1.237  -8.409   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -1.236  -1.731   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.248  -2.226   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.402  -1.484   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.143  -0.165   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.566   1.154   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.473   2.473   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.979   3.793   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       2.638   6.183   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.566   5.111   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.083   5.688   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.330   7.255   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -0.659   8.244   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -0.329   9.728   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       0.000   0.495   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.236   1.236   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -2.225   0.082   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -6.265   1.648   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -4.946   2.390   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -3.709   1.731   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -2.225   2.473   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -2.225   3.957   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -1.401   5.193   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -2.390   6.265   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -2.143   7.749   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      -3.215   8.904   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      -3.792   6.430   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      -3.709   4.616   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -4.946   3.957   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      -6.348   4.616   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -4.121   5.935   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   18                                                  
CONECT    6    5                                                            
CONECT    7    2    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   30                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   32                                                  
CONECT   12   11                                                            
CONECT   13   14                                                            
CONECT   14   13   15   21                                                  
CONECT   15   14   16   24                                                  
CONECT   16   15                                                            
CONECT   17   18                                                            
CONECT   18    5   17   19                                                  
CONECT   19   18   20   26                                                  
CONECT   20    3   19   21                                                  
CONECT   21   14   20   22                                                  
CONECT   22   21   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   15   23   25                                                  
CONECT   25   24                                                            
CONECT   26   19                                                            
CONECT   27   28                                                            
CONECT   28   22   27   29                                                  
CONECT   29   28   30                                                       
CONECT   30    9   29   31                                                  
CONECT   31   30   32   40                                                  
CONECT   32   11   31   33                                                  
CONECT   33   32   35                                                       
CONECT   34   35                                                            
CONECT   35   33   34   36                                                  
CONECT   36   35   37   48                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   50                                                  
CONECT   39   38                                                            
CONECT   40   31   41                                                       
CONECT   41   40   42   46                                                  
CONECT   42   41                                                            
CONECT   43   44                                                            
CONECT   44   43   45   54                                                  
CONECT   45   44   46                                                       
CONECT   46   41   45   47                                                  
CONECT   47   46   48   53                                                  
CONECT   48   36   47   49                                                  
CONECT   49   48   50   56                                                  
CONECT   50   38   49   51                                                  
CONECT   51   50                                                            
CONECT   52   53                                                            
CONECT   53   47   52   54                                                  
CONECT   54   44   53   55                                                  
CONECT   55   54                                                            
CONECT   56   49                                                            
MASTER        0    0    0    0    0    0    0    0   56    0  124    0
END

COMPND    HMDB0256194
HETATM    1  O1  UNL     1       1.869   0.071  -3.686  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.568  -0.062  -2.608  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.642   0.777  -1.638  1.00  0.00           O  
HETATM    4  C2  UNL     1       2.524   1.953  -1.027  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.197   1.936  -0.267  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.369   1.940   1.088  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.227   1.997   1.813  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.364   1.208   2.975  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.061   1.716   1.143  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.006   1.229   2.091  1.00  0.00           O  
HETATM   11  C6  UNL     1      -2.457  -0.036   2.264  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.961  -0.657   3.322  1.00  0.00           O  
HETATM   13  C7  UNL     1      -3.402  -0.814   1.475  1.00  0.00           C  
HETATM   14  C8  UNL     1      -3.261  -2.208   1.500  1.00  0.00           C  
HETATM   15  C9  UNL     1      -4.162  -3.083   0.940  1.00  0.00           C  
HETATM   16  O7  UNL     1      -3.968  -4.449   0.998  1.00  0.00           O  
HETATM   17  C10 UNL     1      -5.282  -2.539   0.313  1.00  0.00           C  
HETATM   18  O8  UNL     1      -6.226  -3.376  -0.266  1.00  0.00           O  
HETATM   19  C11 UNL     1      -5.491  -1.194   0.243  1.00  0.00           C  
HETATM   20  O9  UNL     1      -6.627  -0.742  -0.390  1.00  0.00           O  
HETATM   21  C12 UNL     1      -4.534  -0.326   0.828  1.00  0.00           C  
HETATM   22  C13 UNL     1      -4.875   1.094   0.602  1.00  0.00           C  
HETATM   23  C14 UNL     1      -4.124   2.016  -0.146  1.00  0.00           C  
HETATM   24  C15 UNL     1      -4.605   3.333  -0.243  1.00  0.00           C  
HETATM   25  C16 UNL     1      -5.778   3.695   0.375  1.00  0.00           C  
HETATM   26  O10 UNL     1      -6.281   5.012   0.292  1.00  0.00           O  
HETATM   27  C17 UNL     1      -6.489   2.766   1.093  1.00  0.00           C  
HETATM   28  O11 UNL     1      -7.695   3.174   1.716  1.00  0.00           O  
HETATM   29  C18 UNL     1      -6.059   1.471   1.219  1.00  0.00           C  
HETATM   30  O12 UNL     1      -6.842   0.628   1.960  1.00  0.00           O  
HETATM   31  C19 UNL     1      -2.969   1.726  -0.973  1.00  0.00           C  
HETATM   32  O13 UNL     1      -2.791   2.517  -2.019  1.00  0.00           O  
HETATM   33  O14 UNL     1      -2.032   0.733  -0.825  1.00  0.00           O  
HETATM   34  C20 UNL     1      -0.913   0.700   0.041  1.00  0.00           C  
HETATM   35  C21 UNL     1       0.415   0.661  -0.588  1.00  0.00           C  
HETATM   36  O15 UNL     1       1.170  -0.496  -0.309  1.00  0.00           O  
HETATM   37  C22 UNL     1       2.108  -0.745   0.648  1.00  0.00           C  
HETATM   38  O16 UNL     1       1.730  -1.289   1.776  1.00  0.00           O  
HETATM   39  C23 UNL     1       3.547  -0.495   0.631  1.00  0.00           C  
HETATM   40  C24 UNL     1       4.030   0.218   1.734  1.00  0.00           C  
HETATM   41  C25 UNL     1       5.367   0.522   1.885  1.00  0.00           C  
HETATM   42  O17 UNL     1       5.832   1.233   2.987  1.00  0.00           O  
HETATM   43  C26 UNL     1       6.251   0.114   0.928  1.00  0.00           C  
HETATM   44  O18 UNL     1       7.578   0.439   1.113  1.00  0.00           O  
HETATM   45  C27 UNL     1       5.817  -0.584  -0.162  1.00  0.00           C  
HETATM   46  O19 UNL     1       6.751  -0.971  -1.103  1.00  0.00           O  
HETATM   47  C28 UNL     1       4.446  -0.901  -0.327  1.00  0.00           C  
HETATM   48  C29 UNL     1       4.185  -1.689  -1.541  1.00  0.00           C  
HETATM   49  C30 UNL     1       3.318  -1.327  -2.581  1.00  0.00           C  
HETATM   50  C31 UNL     1       3.220  -2.203  -3.654  1.00  0.00           C  
HETATM   51  C32 UNL     1       3.912  -3.398  -3.771  1.00  0.00           C  
HETATM   52  O20 UNL     1       3.726  -4.186  -4.898  1.00  0.00           O  
HETATM   53  C33 UNL     1       4.760  -3.724  -2.725  1.00  0.00           C  
HETATM   54  O21 UNL     1       5.464  -4.921  -2.830  1.00  0.00           O  
HETATM   55  C34 UNL     1       4.905  -2.902  -1.629  1.00  0.00           C  
HETATM   56  O22 UNL     1       5.759  -3.343  -0.670  1.00  0.00           O  
HETATM   57  H1  UNL     1       3.302   2.175  -0.247  1.00  0.00           H  
HETATM   58  H2  UNL     1       2.584   2.900  -1.655  1.00  0.00           H  
HETATM   59  H3  UNL     1       0.614   2.794  -0.603  1.00  0.00           H  
HETATM   60  H4  UNL     1       0.175   3.059   2.233  1.00  0.00           H  
HETATM   61  H5  UNL     1      -0.284   1.492   3.671  1.00  0.00           H  
HETATM   62  H6  UNL     1      -1.488   2.675   0.784  1.00  0.00           H  
HETATM   63  H7  UNL     1      -2.360  -2.588   2.007  1.00  0.00           H  
HETATM   64  H8  UNL     1      -3.175  -4.910   1.419  1.00  0.00           H  
HETATM   65  H9  UNL     1      -6.178  -4.380  -0.301  1.00  0.00           H  
HETATM   66  H10 UNL     1      -7.299  -1.334  -0.780  1.00  0.00           H  
HETATM   67  H11 UNL     1      -4.071   4.090  -0.798  1.00  0.00           H  
HETATM   68  H12 UNL     1      -5.726   5.676  -0.262  1.00  0.00           H  
HETATM   69  H13 UNL     1      -8.257   2.547   2.248  1.00  0.00           H  
HETATM   70  H14 UNL     1      -6.598  -0.311   2.168  1.00  0.00           H  
HETATM   71  H15 UNL     1      -1.035  -0.302   0.574  1.00  0.00           H  
HETATM   72  H16 UNL     1       0.257   0.683  -1.683  1.00  0.00           H  
HETATM   73  H17 UNL     1       3.390   0.565   2.552  1.00  0.00           H  
HETATM   74  H18 UNL     1       6.815   1.452   3.085  1.00  0.00           H  
HETATM   75  H19 UNL     1       8.330   0.160   0.509  1.00  0.00           H  
HETATM   76  H20 UNL     1       7.720  -0.801  -1.089  1.00  0.00           H  
HETATM   77  H21 UNL     1       2.567  -1.970  -4.480  1.00  0.00           H  
HETATM   78  H22 UNL     1       4.173  -5.054  -5.080  1.00  0.00           H  
HETATM   79  H23 UNL     1       5.391  -5.533  -3.594  1.00  0.00           H  
HETATM   80  H24 UNL     1       5.996  -3.000   0.204  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   49
CONECT    3    4
CONECT    4    5   57   58
CONECT    5    6   35   59
CONECT    6    7
CONECT    7    8    9   60
CONECT    8   61
CONECT    9   10   34   62
CONECT   10   11
CONECT   11   12   12   13
CONECT   13   14   14   21
CONECT   14   15   63
CONECT   15   16   17   17
CONECT   16   64
CONECT   17   18   19
CONECT   18   65
CONECT   19   20   21   21
CONECT   20   66
CONECT   21   22
CONECT   22   23   23   29
CONECT   23   24   31
CONECT   24   25   25   67
CONECT   25   26   27
CONECT   26   68
CONECT   27   28   29   29
CONECT   28   69
CONECT   29   30
CONECT   30   70
CONECT   31   32   32   33
CONECT   33   34
CONECT   34   35   71
CONECT   35   36   72
CONECT   36   37
CONECT   37   38   38   39
CONECT   39   40   40   47
CONECT   40   41   73
CONECT   41   42   43   43
CONECT   42   74
CONECT   43   44   45
CONECT   44   75
CONECT   45   46   47   47
CONECT   46   76
CONECT   47   48
CONECT   48   49   49   55
CONECT   49   50
CONECT   50   51   51   77
CONECT   51   52   53
CONECT   52   78
CONECT   53   54   55   55
CONECT   54   79
CONECT   55   56
CONECT   56   80
END

HMDB0256194
     RDKit          3D
Pedunculagin
 80 86  0  0  0  0  0  0  0  0999 V2000
    1.8693    0.0706   -3.6862 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5683   -0.0625   -2.6082 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6416    0.7765   -1.6379 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5240    1.9529   -1.0272 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1973    1.9356   -0.2666 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3691    1.9402    1.0885 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2269    1.9965    1.8129 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3636    1.2083    2.9753 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0611    1.7158    1.1428 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0062    1.2294    2.0912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4570   -0.0361    2.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9612   -0.6566    3.3217 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4021   -0.8137    1.4745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2610   -2.2084    1.4996 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1619   -3.0828    0.9404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9682   -4.4489    0.9982 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2820   -2.5387    0.3130 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2263   -3.3763   -0.2664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4908   -1.1938    0.2429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6273   -0.7416   -0.3899 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5339   -0.3264    0.8281 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8748    1.0935    0.6019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1236    2.0159   -0.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6048    3.3327   -0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7782    3.6947    0.3751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2814    5.0117    0.2923 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4888    2.7665    1.0931 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6953    3.1743    1.7159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0590    1.4707    1.2188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8423    0.6277    1.9596 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9695    1.7257   -0.9733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7915    2.5174   -2.0185 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0320    0.7330   -0.8252 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9133    0.7000    0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4146    0.6608   -0.5877 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1699   -0.4961   -0.3086 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1083   -0.7449    0.6480 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7301   -1.2886    1.7763 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5475   -0.4945    0.6312 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0298    0.2179    1.7338 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3669    0.5220    1.8853 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8321    1.2325    2.9871 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2514    0.1144    0.9276 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5785    0.4391    1.1135 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8173   -0.5838   -0.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7506   -0.9708   -1.1026 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4458   -0.9011   -0.3269 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1850   -1.6887   -1.5414 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3182   -1.3269   -2.5814 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2196   -2.2026   -3.6541 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9121   -3.3984   -3.7707 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7259   -4.1860   -4.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7600   -3.7237   -2.7251 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4636   -4.9213   -2.8302 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9048   -2.9023   -1.6286 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7590   -3.3433   -0.6696 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3022    2.1752   -0.2467 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5843    2.9005   -1.6547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6139    2.7940   -0.6031 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1748    3.0593    2.2333 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2843    1.4923    3.6713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4885    2.6754    0.7835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3597   -2.5884    2.0067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1747   -4.9102    1.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1775   -4.3802   -0.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2990   -1.3343   -0.7803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0708    4.0900   -0.7982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7262    5.6759   -0.2621 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2571    2.5465    2.2478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5981   -0.3107    2.1678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0354   -0.3020    0.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2574    0.6833   -1.6827 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3903    0.5646    2.5518 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8147    1.4520    3.0849 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3301    0.1605    0.5091 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7196   -0.8015   -1.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5666   -1.9699   -4.4798 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1728   -5.0538   -5.0796 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3908   -5.5328   -3.5942 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9962   -3.0004    0.2043 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
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 52 78  1  0
 54 79  1  0
 56 80  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₃₄H₂₄O₂₂

Average Molecular Weight

784.5412

Monoisotopic Molecular Weight

784.075922452

IUPAC Name

7,8,9,12,13,14,20,28,29,30,33,34,35-tridecahydroxy-3,18,21,24,39-pentaoxaheptacyclo[20.17.0.0²,¹⁹.0⁵,¹⁰.0¹¹,¹⁶.0²⁶,³¹.0³²,³⁷]nonatriaconta-5,7,9,11,13,15,26(31),27,29,32(37),33,35-dodecaene-4,17,25,38-tetrone

Traditional Name

CAS Registry Number

Not Available

SMILES

OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12

InChI Identifier

InChI=1S/C34H24O22/c35-10-1-6-15(23(43)19(10)39)16-7(2-11(36)20(40)24(16)44)31(48)54-27-14(5-52-30(6)47)53-34(51)29-28(27)55-32(49)8-3-12(37)21(41)25(45)17(8)18-9(33(50)56-29)4-13(38)22(42)26(18)46/h1-4,14,27-29,34-46,51H,5H2

InChI Key

IYMHVUYNBVWXKH-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

Hydrolyzable tannin
Tetracarboxylic acid or derivatives
Gallic acid or derivatives
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monosaccharide
Oxane
Carboxylic acid ester
Hemiacetal
Lactone
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (HMDB: HMDB0256194)

Food

Fruit

Berry

Rubus (Blackberry, Raspberry) (FooDB: FOOD00160)
Red raspberry (FooDB: FOOD00162)

Tropical fruit

Guava (FooDB: FOOD00150)
Pomegranate (FooDB: FOOD00151)

Tea

Nut

Walnut (FooDB: FOOD00608)
Acorn (FooDB: FOOD00282)

Herb and spice

Spice

Cloves (FooDB: FOOD00179)

Process

Not Available

Role

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
logP	2.48	ALOGPS
logP	1.95	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	7.25	ChemAxon
pKa (Strongest Basic)	-6.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	13	ChemAxon
Polar Surface Area	377.42 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	177.14 m³·mol⁻¹	ChemAxon
Polarizability	69.1 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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
DeepCCS	[M-2H]-	291.058	30932474
DeepCCS	[M+Na]+	265.078	30932474
AllCCS	[M+H]+	249.2	32859911
AllCCS	[M+H-H2O]+	249.0	32859911
AllCCS	[M+NH4]+	249.3	32859911
AllCCS	[M+Na]+	249.3	32859911
AllCCS	[M-H]-	244.6	32859911
AllCCS	[M+Na-2H]-	247.0	32859911
AllCCS	[M+HCOO]-	249.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Pedunculagin	OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12	9145.3	Standard polar	33892256
Pedunculagin	OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12	5958.1	Standard non polar	33892256
Pedunculagin	OC1OC2COC(=O)C3=C(C(O)=C(O)C(O)=C3)C3=C(C=C(O)C(O)=C3O)C(=O)OC2C2OC(=O)C3=CC(O)=C(O)C(O)=C3C3=C(O)C(O)=C(O)C=C3C(=O)OC12	7271.2	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 - Pedunculagin GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_8) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_9) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_10) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_11) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_12) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TMS_1_13) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_4) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_5) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_6) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_7) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_8) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_9) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_10) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_11) - 70eV, Positive	Not Available	2021-11-05	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Pedunculagin GC-MS (TBDMS_1_12) - 70eV, Positive	Not Available	2021-11-05	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 - Pedunculagin 10V, Positive-QTOF	splash10-00kr-0006501900-3dcd0963de784f9cb74d	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pedunculagin 20V, Positive-QTOF	splash10-0aos-0034201900-c5f23db9105fccdfa06c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pedunculagin 40V, Positive-QTOF	splash10-0a4i-0039101000-7880e6a8fa2b2af9c639	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pedunculagin 10V, Negative-QTOF	splash10-001r-0001000900-52f77d1fb71ef2fd1d26	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pedunculagin 20V, Negative-QTOF	splash10-014s-0004601900-fa682221bc082c2f4f30	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Pedunculagin 40V, Negative-QTOF	splash10-014l-1249100300-62132d6cfa4685bedbb6	2016-08-03	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

FDB012753

KNApSAcK ID

Not Available

Chemspider ID

430988

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Pedunculagin

METLIN ID

Not Available

PubChem Compound

492391

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Pedunculagin (HMDB0256194)

MOL for HMDB0256194 (Pedunculagin)

3D MOL for HMDB0256194 (Pedunculagin)

3D SDF for HMDB0256194 (Pedunculagin)

3D-SDF for HMDB0256194 (Pedunculagin)

PDB for HMDB0256194 (Pedunculagin)

3D PDB for HMDB0256194 (Pedunculagin)

SMILES for HMDB0256194 (Pedunculagin)

INCHI for HMDB0256194 (Pedunculagin)

Structure for HMDB0256194 (Pedunculagin)

3D Structure for HMDB0256194 (Pedunculagin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra