NP-MRD: Showing NP-Card for Silybin A (NP0012443)

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Record Information

Version

1.0

Created at

2021-01-05 21:49:21 UTC

Updated at

2021-08-19 23:59:50 UTC

NP-MRD ID

NP0012443

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Silybin A

Provided By

NPAtlas

Description

Silibinin is also known as silybin or legalon. Silibinin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Silybin A is found in Anastatica hierochuntica and Aspergillus iizukae. It was first documented in 2013 (PMID: 22086675). Based on a literature review a significant number of articles have been published on Silibinin (PMID: 24456525) (PMID: 22555054) (PMID: 22899727) (PMID: 23073223).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117083D          

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M  END

     RDKit          3D

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  Mrv1652306242117083D          

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    5.2883    2.8528   -0.3149 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4670    2.1508   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6626    2.8000   -0.7752 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.1817    2.7693    0.1131 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3161    3.9316   -0.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4992    2.2378   -0.8555 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
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 13 14  2  0  0  0  0
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 18 20  2  0  0  0  0
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  5 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 34  3  1  0  0  0  0
 29  6  1  0  0  0  0
 27  8  1  0  0  0  0
 23 11  1  0  0  0  0
 20 13  1  0  0  0  0
  1 36  1  0  0  0  0
  1 37  1  0  0  0  0
  1 38  1  0  0  0  0
  4 39  1  0  0  0  0
  6 40  1  1  0  0  0
  9 41  1  0  0  0  0
 11 42  1  6  0  0  0
 14 43  1  0  0  0  0
 16 44  1  0  0  0  0
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 23 47  1  1  0  0  0
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 26 50  1  0  0  0  0
 29 51  1  6  0  0  0
 30 52  1  0  0  0  0
 30 53  1  0  0  0  0
 31 54  1  0  0  0  0
 32 55  1  0  0  0  0
 33 56  1  0  0  0  0
 35 57  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0012443

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C(O[H])=C2C(O[C@]([H])(C3=C([H])C([H])=C4O[C@]([H])(C([H])([H])O[H])[C@]([H])(OC4=C3[H])C3=C([H])C([H])=C(O[H])C(OC([H])([H])[H])=C3[H])[C@@]([H])(O[H])C2=O)=C1[H]

> <INCHI_IDENTIFIER>
InChI=1S/C25H22O10/c1-32-17-6-11(2-4-14(17)28)24-20(10-26)33-16-5-3-12(7-18(16)34-24)25-23(31)22(30)21-15(29)8-13(27)9-19(21)35-25/h2-9,20,23-29,31H,10H2,1H3/t20-,23+,24-,25-/m1/s1

> <INCHI_KEY>
SEBFKMXJBCUCAI-HKTJVKLFSA-N

> <FORMULA>
C25H22O10

> <MOLECULAR_WEIGHT>
482.441

> <EXACT_MASS>
482.121296908

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
48.6374535953362

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-3,5,7-trihydroxy-2-[(2R,3R)-3-(4-hydroxy-3-methoxyphenyl)-2-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-3,4-dihydro-2H-1-benzopyran-4-one

> <ALOGPS_LOGP>
2.35

> <JCHEM_LOGP>
2.6293160946666667

> <ALOGPS_LOGS>
-3.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.275274448635567

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.7549598399992865

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9904140611148753

> <JCHEM_POLAR_SURFACE_AREA>
155.14

> <JCHEM_REFRACTIVITY>
120.29390000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.26e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
silibinin

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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  1  2  1  0
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 13 14  2  0
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 21 22  2  0
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 23 24  1  0
 10 25  2  0
 25 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
  5 32  2  0
 32 33  1  0
 33 34  2  0
 34 35  1  0
 34  3  1  0
 29  6  1  0
 27  8  1  0
 23 11  1  0
 20 13  1  0
  1 36  1  0
  1 37  1  0
  1 38  1  0
  4 39  1  0
  6 40  1  1
  9 41  1  0
 11 42  1  6
 14 43  1  0
 16 44  1  0
 17 45  1  0
 19 46  1  0
 23 47  1  1
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 25 49  1  0
 26 50  1  0
 29 51  1  6
 30 52  1  0
 30 53  1  0
 31 54  1  0
 32 55  1  0
 33 56  1  0
 35 57  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       7.732  -1.301  -0.171  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.604   0.077  -0.353  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.428   0.793  -0.229  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.228   0.145   0.105  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.046   0.826   0.236  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.735   0.230   0.579  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.700   0.799  -0.255  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.438   0.284  -0.270  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.725   1.017  -0.424  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.976   0.435  -0.430  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.230   1.206  -0.595  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.038   0.533  -1.507  0.00  0.00           O+0
HETATM   13  C   UNK     0      -5.234  -0.090  -1.270  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.009  -0.613  -2.305  0.00  0.00           C+0
HETATM   15  C   UNK     0      -7.210  -1.237  -2.047  0.00  0.00           C+0
HETATM   16  O   UNK     0      -7.950  -1.744  -3.111  0.00  0.00           O+0
HETATM   17  C   UNK     0      -7.622  -1.330  -0.745  0.00  0.00           C+0
HETATM   18  C   UNK     0      -6.876  -0.820   0.320  0.00  0.00           C+0
HETATM   19  O   UNK     0      -7.369  -0.957   1.599  0.00  0.00           O+0
HETATM   20  C   UNK     0      -5.689  -0.207   0.019  0.00  0.00           C+0
HETATM   21  C   UNK     0      -4.854   0.348   1.073  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.912  -0.098   2.247  0.00  0.00           O+0
HETATM   23  C   UNK     0      -3.922   1.472   0.706  0.00  0.00           C+0
HETATM   24  O   UNK     0      -4.738   2.596   0.532  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.063  -0.933  -0.276  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.908  -1.700  -0.118  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.331  -1.097  -0.115  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.498  -1.787   0.035  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.681  -1.244   0.603  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.842  -1.764   2.038  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.974  -1.253   2.626  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.117   2.212   0.013  0.00  0.00           C+0
HETATM   33  C   UNK     0       5.288   2.853  -0.315  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.467   2.151  -0.442  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.663   2.800  -0.775  0.00  0.00           O+0
HETATM   36  H   UNK     0       8.618  -1.669  -0.751  0.00  0.00           H+0
HETATM   37  H   UNK     0       7.880  -1.620   0.862  0.00  0.00           H+0
HETATM   38  H   UNK     0       6.859  -1.860  -0.602  0.00  0.00           H+0
HETATM   39  H   UNK     0       5.267  -0.915   0.260  0.00  0.00           H+0
HETATM   40  H   UNK     0       2.428   0.581   1.613  0.00  0.00           H+0
HETATM   41  H   UNK     0      -0.643   2.077  -0.543  0.00  0.00           H+0
HETATM   42  H   UNK     0      -2.988   2.210  -1.050  0.00  0.00           H+0
HETATM   43  H   UNK     0      -5.648  -0.518  -3.312  0.00  0.00           H+0
HETATM   44  H   UNK     0      -8.825  -2.205  -2.993  0.00  0.00           H+0
HETATM   45  H   UNK     0      -8.558  -1.815  -0.532  0.00  0.00           H+0
HETATM   46  H   UNK     0      -7.034  -0.681   2.462  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.229   1.706   1.523  0.00  0.00           H+0
HETATM   48  H   UNK     0      -5.692   2.369   0.452  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.002  -1.450  -0.271  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.951  -2.769   0.005  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.506  -1.684   0.021  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.944  -1.409   2.586  0.00  0.00           H+0
HETATM   53  H   UNK     0       2.896  -2.865   1.980  0.00  0.00           H+0
HETATM   54  H   UNK     0       4.727  -1.897   2.540  0.00  0.00           H+0
HETATM   55  H   UNK     0       3.182   2.769   0.113  0.00  0.00           H+0
HETATM   56  H   UNK     0       5.316   3.932  -0.483  0.00  0.00           H+0
HETATM   57  H   UNK     0       8.499   2.238  -0.856  0.00  0.00           H+0
CONECT    1    2   36   37   38                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5   39                                                  
CONECT    5    4    6   32                                                  
CONECT    6    5    7   29   40                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   27                                                  
CONECT    9    8   10   41                                                  
CONECT   10    9   11   25                                                  
CONECT   11   10   12   23   42                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   43                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15   44                                                       
CONECT   17   15   18   45                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18   46                                                       
CONECT   20   18   21   13                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   11   47                                             
CONECT   24   23   48                                                       
CONECT   25   10   26   49                                                  
CONECT   26   25   27   50                                                  
CONECT   27   26   28    8                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30    6   51                                             
CONECT   30   29   31   52   53                                             
CONECT   31   30   54                                                       
CONECT   32    5   33   55                                                  
CONECT   33   32   34   56                                                  
CONECT   34   33   35    3                                                  
CONECT   35   34   57                                                       
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    1                                                            
CONECT   39    4                                                            
CONECT   40    6                                                            
CONECT   41    9                                                            
CONECT   42   11                                                            
CONECT   43   14                                                            
CONECT   44   16                                                            
CONECT   45   17                                                            
CONECT   46   19                                                            
CONECT   47   23                                                            
CONECT   48   24                                                            
CONECT   49   25                                                            
CONECT   50   26                                                            
CONECT   51   29                                                            
CONECT   52   30                                                            
CONECT   53   30                                                            
CONECT   54   31                                                            
CONECT   55   32                                                            
CONECT   56   33                                                            
CONECT   57   35                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  122    0
END

RDKit          3D

57 61  0  0  0  0  0  0  0  0999 V2000
    7.7318   -1.3014   -0.1708 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6043    0.0774   -0.3534 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4279    0.7927   -0.2292 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2281    0.1449    0.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0458    0.8256    0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7351    0.2295    0.5787 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7000    0.7985   -0.2550 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4379    0.2836   -0.2696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7246    1.0172   -0.4243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9757    0.4351   -0.4304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2304    1.2058   -0.5949 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.0383    0.5325   -1.5067 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2339   -0.0902   -1.2697 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0093   -0.6130   -2.3052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2104   -1.2372   -2.0473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9503   -1.7439   -3.1114 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6217   -1.3296   -0.7448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8757   -0.8195    0.3203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3689   -0.9573    1.5985 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6885   -0.2074    0.0190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8537    0.3482    1.0731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9121   -0.0981    2.2468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9219    1.4719    0.7064 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.7381    2.5962    0.5315 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -0.9326   -0.2757 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9076   -1.6995   -0.1176 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3311   -1.0973   -0.1146 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4984   -1.7867    0.0352 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6812   -1.2435    0.6028 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8418   -1.7643    2.0377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9735   -1.2527    2.6257 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1175    2.2121    0.0125 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2883    2.8528   -0.3149 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4670    2.1508   -0.4416 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6626    2.8000   -0.7752 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6184   -1.6689   -0.7512 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8805   -1.6202    0.8622 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8586   -1.8604   -0.6019 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2671   -0.9149    0.2598 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4275    0.5814    1.6129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6432    2.0774   -0.5434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9878    2.2098   -1.0500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6477   -0.5178   -3.3122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8247   -2.2052   -2.9930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5581   -1.8151   -0.5323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0340   -0.6806    2.4625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2293    1.7057    1.5228 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6924    2.3686    0.4517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0025   -1.4498   -0.2710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9514   -2.7691    0.0048 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5060   -1.6839    0.0206 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9445   -1.4086    2.5864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8963   -2.8650    1.9798 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7266   -1.8972    2.5402 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1817    2.7693    0.1131 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3161    3.9316   -0.4829 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4992    2.2378   -0.8555 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
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  2  0
 17 18  1  0
 18 19  1  0
 18 20  2  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  1  0
 10 25  2  0
 25 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
  5 32  2  0
 32 33  1  0
 33 34  2  0
 34 35  1  0
 34  3  1  0
 29  6  1  0
 27  8  1  0
 23 11  1  0
 20 13  1  0
  1 36  1  0
  1 37  1  0
  1 38  1  0
  4 39  1  0
  6 40  1  1
  9 41  1  0
 11 42  1  6
 14 43  1  0
 16 44  1  0
 17 45  1  0
 19 46  1  0
 23 47  1  1
 24 48  1  0
 25 49  1  0
 26 50  1  0
 29 51  1  6
 30 52  1  0
 30 53  1  0
 31 54  1  0
 32 55  1  0
 33 56  1  0
 35 57  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Flavobin	ChEBI
Karsil	ChEBI
Silibinina	ChEBI
Silibinine	ChEBI
Silibininum	ChEBI
Silybin	ChEBI
Silymarin	ChEBI
Silymarin I	Kegg
Legalon	Kegg
2,3 Dehydrosilybin	MeSH
2,3-Dehydrosilybin	MeSH
Alepa forte	MeSH
Alepa-forte	MeSH
Ardeyhepan	MeSH
Cefasilymarin	MeSH
Hepa merz sil	MeSH
Hepa loges	MeSH
Hepa-merz sil	MeSH
HepaBesch	MeSH
Hepar pasc	MeSH
Hepar-pasc	MeSH
Heparsyx	MeSH
Heplant	MeSH
Lagosa	MeSH
Silibinin a	MeSH
Silibinin b	MeSH
Durasilymarin	MeSH
Hepa-loges	MeSH
Legalon forte	MeSH
Silibin	MeSH
Silybin a	MeSH
Silybin b	MeSH
Silybinin	MeSH
Silibinin	MeSH
Hepatos	MeSH

Chemical Formula

C₂₅H₂₂O₁₀

Average Mass

482.4410 Da

Monoisotopic Mass

482.12130 Da

IUPAC Name

(2R,3R)-3,5,7-trihydroxy-2-[(2R,3R)-3-(4-hydroxy-3-methoxyphenyl)-2-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-3,4-dihydro-2H-1-benzopyran-4-one

Traditional Name

silibinin

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=CC(=C1)[C@H]1OC2=C(O[C@@H]1CO)C=CC(=C2)[C@H]1OC2=CC(O)=CC(O)=C2C(=O)[C@@H]1O

InChI Identifier

InChI=1S/C25H22O10/c1-32-17-6-11(2-4-14(17)28)24-20(10-26)33-16-5-3-12(7-18(16)34-24)25-23(31)22(30)21-15(29)8-13(27)9-19(21)35-25/h2-9,20,23-29,31H,10H2,1H3/t20-,23+,24-,25-/m1/s1

InChI Key

SEBFKMXJBCUCAI-HKTJVKLFSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anastatica hierochuntica	LOTUS Database	35616633
Aspergillus iizukae	NPAtlas	24456525
Silybum marianum	KNApSAcK Database	22123792

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as flavonolignans. These are non-conventional lignans that derived from flavonoids. They are characterized by a p-dioxin ring substituted at one carbon atom by a C3C6 (phenylpropan) group and fused to the B-ring of the 2-phenylchromene moiety.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Flavonolignans

Sub Class

Not Available

Direct Parent

Flavonolignans

Alternative Parents

Substituents

Flavonolignan
Hydroxyflavonoid
3-hydroxyflavonoid
Flavanonol
Flavanone
7-hydroxyflavonoid
5-hydroxyflavonoid
Flavan
Phenylbenzodioxane
2-phenylbenzo-1,4-dioxane
Chromone
1-benzopyran
Methoxyphenol
Benzopyran
Chromane
Benzodioxane
Benzo-1,4-dioxane
Phenoxy compound
Anisole
Methoxybenzene
Aryl alkyl ketone
Aryl ketone
Phenol ether
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Para-dioxin
Monocyclic benzene moiety
Vinylogous acid
Secondary alcohol
Ketone
Polyol
Organoheterocyclic compound
Ether
Oxacycle
Alcohol
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

aromatic ether (CHEBI:9144 )
polyphenol (CHEBI:9144 )
benzodioxine (CHEBI:9144 )
flavonolignan (CHEBI:9144 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	793.03 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	77.36 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	4.232 (est)	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	2.35	ALOGPS
logP	2.63	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	7.75	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	155.14 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	120.29 m³·mol⁻¹	ChemAxon
Polarizability	48.64 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA001288

HMDB ID

Not Available

DrugBank ID

DB09298

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00001003

Chemspider ID

29263

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Silibinin

METLIN ID

Not Available

PubChem Compound

31553

PDB ID

Not Available

ChEBI ID

9144

Good Scents ID

rw1108841

References

General References

El-Elimat T, Raja HA, Graf TN, Faeth SH, Cech NB, Oberlies NH: Flavonolignans from Aspergillus iizukae, a fungal endophyte of milk thistle (Silybum marianum). J Nat Prod. 2014 Feb 28;77(2):193-9. doi: 10.1021/np400955q. Epub 2014 Jan 23. [PubMed:24456525 ]
Raina K, Agarwal C, Agarwal R: Effect of silibinin in human colorectal cancer cells: targeting the activation of NF-kappaB signaling. Mol Carcinog. 2013 Mar;52(3):195-206. doi: 10.1002/mc.21843. Epub 2011 Nov 15. [PubMed:22086675 ]
Ward J, Kapadia K, Brush E, Salhanick SD: Amatoxin poisoning: case reports and review of current therapies. J Emerg Med. 2013 Jan;44(1):116-21. doi: 10.1016/j.jemermed.2012.02.020. Epub 2012 May 1. [PubMed:22555054 ]
Chtourou Y, Garoui E, Boudawara T, Zeghal N: Therapeutic efficacy of silymarin from milk thistle in reducing manganese-induced hepatic damage and apoptosis in rats. Hum Exp Toxicol. 2013 Jan;32(1):70-81. doi: 10.1177/0960327112455674. Epub 2012 Aug 16. [PubMed:22899727 ]
Barcena R, Moreno A, Rodriguez-Gandia MA, Albillos A, Arocena C, Blesa C, Garcia-Hoz F, Graus J, Nuno J, Lopez-Hervas P, Gajate L, Martinez A, Bermejo T, Mateos ML, Del Campo S: Safety and anti-HCV effect of prolonged intravenous silibinin in HCV genotype 1 subjects in the immediate liver transplant period. J Hepatol. 2013 Mar;58(3):421-6. doi: 10.1016/j.jhep.2012.10.009. Epub 2012 Oct 13. [PubMed:23073223 ]

Showing NP-Card for Silybin A (NP0012443)

MOL for NP0012443 (Silybin A)

3D MOL for NP0012443 (Silybin A)

3D SDF for NP0012443 (Silybin A)

3D-SDF for NP0012443 (Silybin A)

PDB for NP0012443 (Silybin A)

3D PDB for NP0012443 (Silybin A)

SMILES for NP0012443 (Silybin A)

INCHI for NP0012443 (Silybin A)

Structure for NP0012443 (Silybin A)

3D Structure for NP0012443 (Silybin A)