NP-MRD: Showing NP-Card for (2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate (NP0213452)

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Record Information

Version

2.0

Created at

2022-09-05 12:26:35 UTC

Updated at

2022-09-05 12:26:35 UTC

NP-MRD ID

NP0213452

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate

Description

Sibiricaxanthone F belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. (2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate is found in Polygala sibirica. (2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate was first documented in 2011 (PMID: 21803667). Based on a literature review a small amount of articles have been published on Sibiricaxanthone F (PMID: 22819207) (PMID: 22667146).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052214262D          

 45 49  0  0  1  0            999 V2000
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.4302   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1434   -3.7125    0.0000 O   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  1  0  0  0  0
  4  5  2  0  0  0  0
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  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
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  8 17  1  0  0  0  0
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 31 30  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  0  0  0  0
 35 36  1  6  0  0  0
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 37 38  1  1  0  0  0
 37 39  1  0  0  0  0
 31 39  1  0  0  0  0
 39 40  1  1  0  0  0
 29 41  1  0  0  0  0
 23 41  1  0  0  0  0
 41 42  1  1  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  2  0  0  0  0
M  END

     RDKit          3D

 79 83  0  0  0  0  0  0  0  0999 V2000
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    3.8744    0.3592   -0.3244 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2  3  1  0
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 13 51  1  0
 13 52  1  0
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 10 50  1  0
  4 49  1  0
M  END


  Mrv1652309052214262D          

 45 49  0  0  1  0            999 V2000
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5724   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -7.8375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -7.4250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   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  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  2  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
  3 21  2  0  0  0  0
 21 22  1  0  0  0  0
 23 22  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 27 28  1  6  0  0  0
 27 29  1  0  0  0  0
 29 30  1  1  0  0  0
 31 30  1  6  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  0  0  0  0
 35 36  1  6  0  0  0
 35 37  1  0  0  0  0
 37 38  1  1  0  0  0
 37 39  1  0  0  0  0
 31 39  1  0  0  0  0
 39 40  1  1  0  0  0
 29 41  1  0  0  0  0
 23 41  1  0  0  0  0
 41 42  1  1  0  0  0
 42 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0213452

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O[C@@H]3O[C@@H](C)[C@H](O)[C@@H](O)[C@H]3O)[C@H]2OC(C)=O)C=C2OC3=CC(O)=C(OC)C(O)=C3C(=O)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H34O16/c1-9-19(32)23(36)24(37)28(40-9)45-26-20(33)10(2)41-29(27(26)42-11(3)30)44-16-8-14-12(6-15(16)38-4)21(34)18-17(43-14)7-13(31)25(39-5)22(18)35/h6-10,19-20,23-24,26-29,31-33,35-37H,1-5H3/t9-,10-,19-,20-,23+,24+,26+,27+,28-,29-/m0/s1

> <INCHI_KEY>
PDAICPAHYGWJHH-AHQRDZLWSA-N

> <FORMULA>
C29H34O16

> <MOLECULAR_WEIGHT>
638.575

> <EXACT_MASS>
638.184685015

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
62.54019321966707

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5S,6S)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxo-9H-xanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate

> <JCHEM_LOGP>
0.8796433286666661

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.653445793610288

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.076544569472947

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612182608994826

> <JCHEM_POLAR_SURFACE_AREA>
229.35999999999996

> <JCHEM_REFRACTIVITY>
146.30720000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5S,6S)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.000 -13.860   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.334 -16.170   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -4.001 -14.630   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   19                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   17                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16    8   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18    5   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20    3   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   41                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   41                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   39                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   31   40                                                  
CONECT   40   39                                                            
CONECT   41   29   23   42                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43                                                            
MASTER        0    0    0    0    0    0    0    0   45    0   98    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₄O₁₆

Average Mass

638.5750 Da

Monoisotopic Mass

638.18469 Da

IUPAC Name

(2S,3R,4R,5S,6S)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxo-9H-xanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate

Traditional Name

(2S,3R,4R,5S,6S)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

COC1=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O[C@@H]3O[C@@H](C)[C@H](O)[C@@H](O)[C@H]3O)[C@H]2OC(C)=O)C=C2OC3=CC(O)=C(OC)C(O)=C3C(=O)C2=C1

InChI Identifier

InChI=1S/C29H34O16/c1-9-19(32)23(36)24(37)28(40-9)45-26-20(33)10(2)41-29(27(26)42-11(3)30)44-16-8-14-12(6-15(16)38-4)21(34)18-17(43-14)7-13(31)25(39-5)22(18)35/h6-10,19-20,23-24,26-29,31-33,35-37H,1-5H3/t9-,10-,19-,20-,23+,24+,26+,27+,28-,29-/m0/s1

InChI Key

PDAICPAHYGWJHH-AHQRDZLWSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Polygala sibirica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Phenolic glycoside
Xanthone
Chromone
Disaccharide
Glycosyl compound
O-glycosyl compound
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Benzenoid
Oxane
Pyran
Heteroaromatic compound
Vinylogous acid
Carboxylic acid ester
Secondary alcohol
Monocarboxylic acid or derivatives
Oxacycle
Ether
Acetal
Carboxylic acid derivative
Polyol
Organooxygen compound
Alcohol
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	0.88	ChemAxon
pKa (Strongest Acidic)	8.08	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	229.36 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	146.31 m³·mol⁻¹	ChemAxon
Polarizability	62.54 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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

54575712

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Song Y, Yang X, Jiang Y, Tu P: Characterization of the metabolism of sibiricaxanthone F and its aglycone in vitro by high performance liquid chromatography coupled with Q-trap mass spectrometry. J Pharm Biomed Anal. 2012 Nov;70:700-7. doi: 10.1016/j.jpba.2012.06.038. Epub 2012 Jul 3. [PubMed:22819207 ]
Song Y, Jiang Y, Bi D, Tian X, Liang L, Tu P: [Chemical constituents from n-butanol extract of aerial part of Polygala sibirica]. Zhongguo Zhong Yao Za Zhi. 2012 Feb;37(4):471-4. [PubMed:22667146 ]
Yang X, Zhou G, Zou P, Ning Y, Zan K, Tu P, Jiang Y: A rapid and sensitive HPLC-MS/MS analysis and preliminary pharmacokinetic characterization of sibiricaxanthone F in rats. J Chromatogr B Analyt Technol Biomed Life Sci. 2011 Sep 1;879(25):2513-8. doi: 10.1016/j.jchromb.2011.07.002. Epub 2011 Jul 18. [PubMed:21803667 ]
LOTUS database [Link]

Showing NP-Card for (2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate (NP0213452)

MOL for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

3D MOL for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

3D SDF for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

3D-SDF for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

PDB for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

3D PDB for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

SMILES for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

INCHI for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

Structure for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)

3D Structure for NP0213452 ((2s,3r,4r,5s,6s)-2-[(6,8-dihydroxy-2,7-dimethoxy-9-oxoxanthen-3-yl)oxy]-5-hydroxy-6-methyl-4-{[(2s,3r,4r,5r,6s)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}oxan-3-yl acetate)