NP-MRD: Showing NP-Card for Ginsenoside Rk3 (NP0073501)

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Record Information

Version

1.0

Created at

2022-04-28 18:44:32 UTC

Updated at

2022-04-28 18:44:32 UTC

NP-MRD ID

NP0073501

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Ginsenoside Rk3

Description

Ginsenoside Rk3 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Ginsenoside Rk3 is found in Panax ginseng and Panax ginseng C.A.Meyer . It was first documented in 2021 (PMID: 34671254). Based on a literature review a significant number of articles have been published on Ginsenoside Rk3 (PMID: 35310026) (PMID: 34697654) (PMID: 34415764) (PMID: 34397062).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282220442D          

 44 48  0  0  1  0            999 V2000
    3.1838    0.8922    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9035    1.6682    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0914    1.8134    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5596    1.1827    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8399    0.4067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6520    0.2615    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9323   -0.5144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4005   -1.1451    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6808   -1.9210    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1490   -2.5517    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3369   -2.4065    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0566   -1.6306    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5884   -0.9999    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2444   -1.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2874   -2.1161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.8792   -0.0697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3399    1.2325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
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  8 13  1  0  0  0  0
 12 14  1  1  0  0  0
 14 15  1  0  0  0  0
 11 16  1  6  0  0  0
 10 17  1  1  0  0  0
  9 18  1  6  0  0  0
  4 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 22  1  6  0  0  0
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 25 26  1  0  0  0  0
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 24 27  1  6  0  0  0
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 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 19 35  1  1  0  0  0
  4 36  1  6  0  0  0
  2 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  1 40  1  0  0  0  0
 40 41  1  0  0  0  0
 40 42  1  0  0  0  0
 39 43  1  6  0  0  0
  2 44  1  6  0  0  0
M  END

     RDKit          3D

104108  0  0  0  0  0  0  0  0999 V2000
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 42100  1  0
 42101  1  0
 44102  1  0
 44103  1  0
 44104  1  0
 31 89  1  6
 33 90  1  6
 34 91  1  0
 34 92  1  0
 35 93  1  0
 36 94  1  1
 37 95  1  0
 38 96  1  6
 39 97  1  0
 40 98  1  1
 41 99  1  0
M  END


  Mrv1652304282220442D          

 44 48  0  0  1  0            999 V2000
    3.1838    0.8922    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9035    1.6682    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0914    1.8134    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5596    1.1827    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8399    0.4067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6520    0.2615    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9323   -0.5144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4005   -1.1451    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6808   -1.9210    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1490   -2.5517    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3369   -2.4065    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0566   -1.6306    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5884   -0.9999    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2444   -1.4854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2874   -2.1161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8050   -3.0372    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4293   -3.3277    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4929   -2.0662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7475    1.3279    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4672    2.1038    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9990    2.7345    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8111    2.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7187    3.5104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3574    2.0770    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5867    1.2845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0962    0.8215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8637    2.7283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5528    3.4925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810    2.6155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1873    3.2668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0046    3.1540    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5109    3.8053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3282    3.6924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2000    4.5695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9451    0.5269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2487    0.4185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4354    2.2989    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2475    2.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5278    1.3777    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9960    0.7470    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6077    0.1935    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8792   -0.0697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3399    1.2325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6232    2.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  7  1  1  0  0  0
  8  9  1  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
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 12 14  1  1  0  0  0
 14 15  1  0  0  0  0
 11 16  1  6  0  0  0
 10 17  1  1  0  0  0
  9 18  1  6  0  0  0
  4 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 22  1  6  0  0  0
 21 23  1  6  0  0  0
 20 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 19 26  1  0  0  0  0
 24 27  1  6  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 19 35  1  1  0  0  0
  4 36  1  6  0  0  0
  2 37  1  0  0  0  0
 37 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  1 40  1  0  0  0  0
 40 41  1  0  0  0  0
 40 42  1  0  0  0  0
 39 43  1  6  0  0  0
  2 44  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0073501

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCCC(=C)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)CC[C@H](O)C(C)(C)[C@@H]3[C@H](C[C@@]21C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C36H60O8/c1-19(2)10-9-11-20(3)21-12-15-35(7)27(21)22(38)16-25-34(6)14-13-26(39)33(4,5)31(34)23(17-36(25,35)8)43-32-30(42)29(41)28(40)24(18-37)44-32/h10,21-32,37-42H,3,9,11-18H2,1-2,4-8H3/t21-,22-,23+,24-,25-,26+,27+,28-,29+,30-,31+,32-,34-,35-,36-/m1/s1

> <INCHI_KEY>
AVXFIVJSCUOFNT-QXPABTKOSA-N

> <FORMULA>
C36H60O8

> <MOLECULAR_WEIGHT>
620.868

> <EXACT_MASS>
620.428818892

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
104

> <JCHEM_AVERAGE_POLARIZABILITY>
71.61590655700033

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methylhepta-1,5-dien-2-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-8-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
3.22

> <JCHEM_LOGP>
3.419898776333332

> <ALOGPS_LOGS>
-4.22

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.188126658752765

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.209174729361132

> <JCHEM_PKA_STRONGEST_BASIC>
-0.44687266557652705

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
169.33710000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.73e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S,6R)-2-{[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methylhepta-1,5-dien-2-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-8-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       5.474  -0.960   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.481  -2.138   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.004  -3.586   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.011  -4.763   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.495  -4.492   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.972  -3.044   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.965  -1.866   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       0.456  -2.773   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -0.536  -3.950   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.503  -5.669   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.535  -6.212   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.520  -3.857   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.342   6.553   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.032   6.519   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -3.138   4.882   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.083   6.098   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -5.609   5.887   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.554   7.103   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -8.079   6.893   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -5.973   8.530   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.764   0.984   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.331   0.781   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       7.929   4.020   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       8.601   0.361   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       7.241  -0.130   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
CONECT    1    2    6   40                                                  
CONECT    2    1    3   37   44                                             
CONECT    3    2    4   22                                                  
CONECT    4    3    5   19   36                                             
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   18                                                  
CONECT   10    9   11   17                                                  
CONECT   11   10   12   16                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12    8                                                       
CONECT   14   12   15                                                       
CONECT   15   14                                                            
CONECT   16   11                                                            
CONECT   17   10                                                            
CONECT   18    9                                                            
CONECT   19    4   20   26   35                                             
CONECT   20   19   21   24                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21    3                                                       
CONECT   23   21                                                            
CONECT   24   20   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25   19                                                       
CONECT   27   24   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   19                                                            
CONECT   36    4                                                            
CONECT   37    2   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   43                                                  
CONECT   40   39    1   41   42                                             
CONECT   41   40                                                            
CONECT   42   40                                                            
CONECT   43   39                                                            
CONECT   44    2                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   96    0
END

View in JSmol

Synonyms

Value	Source
3beta,12beta-Dihydroxydammar-20(21),24-diene-3-O-beta-D-glucopyranosyl(1-2)-beta-D-glucopyranoside	MeSH

Chemical Formula

C₃₆H₆₀O₈

Average Mass

620.8680 Da

Monoisotopic Mass

620.42882 Da

IUPAC Name

(2R,3R,4S,5S,6R)-2-{[(1R,2R,5S,7R,8S,10R,11R,14S,15R,16R)-5,16-dihydroxy-2,6,6,10,11-pentamethyl-14-(6-methylhepta-1,5-dien-2-yl)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-8-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

CAS Registry Number

Not Available

SMILES

CC(C)=CCCC(=C)[C@H]1CC[C@]2(C)[C@@H]1[C@H](O)C[C@@H]1[C@@]3(C)CC[C@H](O)C(C)(C)[C@@H]3[C@H](C[C@@]21C)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C36H60O8/c1-19(2)10-9-11-20(3)21-12-15-35(7)27(21)22(38)16-25-34(6)14-13-26(39)33(4,5)31(34)23(17-36(25,35)8)43-32-30(42)29(41)28(40)24(18-37)44-32/h10,21-32,37-42H,3,9,11-18H2,1-2,4-8H3/t21-,22-,23+,24-,25-,26+,27+,28-,29+,30-,31+,32-,34-,35-,36-/m1/s1

InChI Key

AVXFIVJSCUOFNT-QXPABTKOSA-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
Panax ginseng	LOTUS Database	35616633
Panax ginseng C.A.Meyer	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
3-hydroxysteroid
14-alpha-methylsteroid
12-hydroxysteroid
Hydroxysteroid
3-beta-hydroxysteroid
Steroid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Monosaccharide
Cyclic alcohol
Secondary alcohol
Polyol
Oxacycle
Acetal
Organoheterocyclic compound
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental 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

Predicted Properties

Property	Value	Source
logP	3.22	ALOGPS
logP	3.42	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-0.45	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	139.84 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	169.34 m³·mol⁻¹	ChemAxon
Polarizability	71.62 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00033881

Chemspider ID

30783491

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

75412555

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Hao F, Pang X, Xu K, Wang M, Ma Z, Tan H, Han L, Chang C, Chen M, Huang Z, Gao Y: Anaphylactic Rare Saponins Separated from Panax notoginseng Saponin and a Proteomic Approach to Their Anaphylactic Mechanism. Evid Based Complement Alternat Med. 2022 Mar 11;2022:7565177. doi: 10.1155/2022/7565177. eCollection 2022. [PubMed:35310026 ]
Wang C, Pang X, Zhu T, Ma S, Liang Y, Zhang Y, Lan X, Wang T, Han L: Rapid discovery of potential ADR compounds from injection of total saponins from Panax notoginseng using data-independent acquisition untargeted metabolomics. Anal Bioanal Chem. 2022 Jan;414(2):1081-1093. doi: 10.1007/s00216-021-03734-5. Epub 2021 Oct 26. [PubMed:34697654 ]
Wan S, Liu Y, Shi J, Fan D, Li B: Anti-Photoaging and Anti-Inflammatory Effects of Ginsenoside Rk3 During Exposure to UV Irradiation. Front Pharmacol. 2021 Oct 4;12:716248. doi: 10.3389/fphar.2021.716248. eCollection 2021. [PubMed:34671254 ]
Qu L, Ma X, Fan D: Ginsenoside Rk3 Suppresses Hepatocellular Carcinoma Development through Targeting the Gut-Liver Axis. J Agric Food Chem. 2021 Sep 8;69(35):10121-10137. doi: 10.1021/acs.jafc.1c03279. Epub 2021 Aug 20. [PubMed:34415764 ]
Qu L, Fu R, Ma X, Fan D: Hepatoprotective effects of ginsenoside Rk3 in acetaminophen-induced liver injury in mice by activation of autophagy. Food Funct. 2021 Oct 4;12(19):9128-9140. doi: 10.1039/d1fo02081a. [PubMed:34397062 ]

Showing NP-Card for Ginsenoside Rk3 (NP0073501)

MOL for NP0073501 (Ginsenoside Rk3)

3D MOL for NP0073501 (Ginsenoside Rk3)

3D SDF for NP0073501 (Ginsenoside Rk3)

3D-SDF for NP0073501 (Ginsenoside Rk3)

PDB for NP0073501 (Ginsenoside Rk3)

3D PDB for NP0073501 (Ginsenoside Rk3)

SMILES for NP0073501 (Ginsenoside Rk3)

INCHI for NP0073501 (Ginsenoside Rk3)

Structure for NP0073501 (Ginsenoside Rk3)

3D Structure for NP0073501 (Ginsenoside Rk3)