NP-MRD: Showing NP-Card for 6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one (NP0264960)

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Record Information

Version

2.0

Created at

2022-09-08 08:46:07 UTC

Updated at

2022-09-08 08:46:08 UTC

NP-MRD ID

NP0264960

Secondary Accession Numbers

None

Natural Product Identification

Common Name

6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

Description

Vaccarin belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. 6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one was first documented in 2021 (PMID: 34303666). Based on a literature review a small amount of articles have been published on Vaccarin (PMID: 33545852) (PMID: 36100252) (PMID: 35961560).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082210462D          

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M  END

     RDKit          3D

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 43 83  1  6
 44 84  1  0
 45 85  1  6
 46 86  1  0
 47 87  1  1
 48 88  1  0
 27 69  1  0
 25 68  1  0
 19 64  1  1
 20 65  1  0
 17 62  1  1
 18 63  1  0
 15 60  1  1
 16 61  1  0
M  END


  Mrv1652309082210462D          

 51 56  0  0  1  0            999 V2000
    1.4289   -2.4750    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
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    3.3000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    3.3000    0.0000 C   0  0  2  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    2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.0000    0.0000 O   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
    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    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  2  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  1  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
    3.5724   -3.7125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  1  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
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 O   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
  1  2  2  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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 10 19  1  0  0  0  0
 19 20  1  1  0  0  0
  8 21  1  0  0  0  0
 21 22  2  0  0  0  0
  5 22  1  0  0  0  0
  4 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  6  0  0  0
 32 33  1  0  0  0  0
 31 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
 36 37  1  6  0  0  0
 36 38  1  0  0  0  0
 29 38  1  0  0  0  0
 38 39  1  1  0  0  0
 40 39  1  6  0  0  0
 40 41  1  0  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 43 44  1  6  0  0  0
 43 45  1  0  0  0  0
 45 46  1  6  0  0  0
 45 47  1  0  0  0  0
 40 47  1  0  0  0  0
 47 48  1  1  0  0  0
 28 49  1  0  0  0  0
 49 50  1  0  0  0  0
 49 51  2  0  0  0  0
  2 51  1  0  0  0  0
 24 51  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0264960

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC=C(C=C2)C2=CC(=O)C3=C(O)C(C4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O[C@@H]4OC[C@H](O)[C@H](O)[C@H]4O)=C(O)C=C3O2)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C32H38O19/c33-7-17-23(40)26(43)30(51-31-27(44)21(38)14(37)9-46-31)29(49-17)20-13(36)6-16-19(24(20)41)12(35)5-15(48-16)10-1-3-11(4-2-10)47-32-28(45)25(42)22(39)18(8-34)50-32/h1-6,14,17-18,21-23,25-34,36-45H,7-9H2/t14-,17+,18+,21-,22+,23+,25-,26-,27+,28+,29?,30+,31-,32+/m0/s1

> <INCHI_KEY>
GYIKGLVKALOGDP-QYUWKIGISA-N

> <FORMULA>
C32H38O19

> <MOLECULAR_WEIGHT>
726.637

> <EXACT_MASS>
726.200729004

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
89

> <JCHEM_AVERAGE_POLARIZABILITY>
70.26918483816084

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-[(3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

> <JCHEM_LOGP>
-3.459200568333333

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.755505512487845

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.138711750898266

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483953456291944

> <JCHEM_POLAR_SURFACE_AREA>
315.21

> <JCHEM_REFRACTIVITY>
164.62740000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
6-[(3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -6.668   8.470   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -4.001   8.470   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.667   6.160   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      13.337  -3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM   47  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   48  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   51                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   23                                                  
CONECT    5    4    6   22                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   21                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   10   20                                                  
CONECT   20   19                                                            
CONECT   21    8   22                                                       
CONECT   22   21    5                                                       
CONECT   23    4   24                                                       
CONECT   24   23   25   51                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   49                                                  
CONECT   29   28   30   38                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   31   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   29   39                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41   47                                                  
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46   47                                                  
CONECT   46   45                                                            
CONECT   47   45   40   48                                                  
CONECT   48   47                                                            
CONECT   49   28   50   51                                                  
CONECT   50   49                                                            
CONECT   51   49    2   24                                                  
MASTER        0    0    0    0    0    0    0    0   51    0  112    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₂H₃₈O₁₉

Average Mass

726.6370 Da

Monoisotopic Mass

726.20073 Da

IUPAC Name

6-[(3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-4H-chromen-4-one

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC=C(C=C2)C2=CC(=O)C3=C(O)C(C4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O[C@@H]4OC[C@H](O)[C@H](O)[C@H]4O)=C(O)C=C3O2)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C32H38O19/c33-7-17-23(40)26(43)30(51-31-27(44)21(38)14(37)9-46-31)29(49-17)20-13(36)6-16-19(24(20)41)12(35)5-15(48-16)10-1-3-11(4-2-10)47-32-28(45)25(42)22(39)18(8-34)50-32/h1-6,14,17-18,21-23,25-34,36-45H,7-9H2/t14-,17+,18+,21-,22+,23+,25-,26-,27+,28+,29?,30+,31-,32+/m0/s1

InChI Key

GYIKGLVKALOGDP-QYUWKIGISA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
Flavonoid-4p-o-glycoside
Flavonoid c-glycoside
Hydroxyflavonoid
Flavone
7-hydroxyflavonoid
5-hydroxyflavonoid
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Disaccharide
Chromone
C-glycosyl compound
1-benzopyran
Benzopyran
Phenoxy compound
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Oxane
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Dialkyl ether
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
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	-3.5	ChemAxon
pKa (Strongest Acidic)	6.14	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	315.21 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	164.63 m³·mol⁻¹	ChemAxon
Polarizability	70.27 Å³	ChemAxon
Number of Rings	6	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

C00014037

Chemspider ID

82963570

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122173223

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Sun JN, Yu XY, Hou B, Ai M, Qi MT, Ma XY, Cai MJ, Gao M, Cai WW, Ni LL, Xu F, Zhou YT, Qiu LY: Vaccarin enhances intestinal barrier function in type 2 diabetic mice. Eur J Pharmacol. 2021 Oct 5;908:174375. doi: 10.1016/j.ejphar.2021.174375. Epub 2021 Jul 22. [PubMed:34303666 ]
Chen Y, Wang Q, Li D, Mensah A, Qiu Y, Ke H, Wei Q: Mussel-inspired double cross-linked hydrogels with desirable mechanical properties, strong tissue-adhesiveness, self-healing properties and antibacterial properties. Mater Sci Eng C Mater Biol Appl. 2021 Jan;120:111690. doi: 10.1016/j.msec.2020.111690. Epub 2020 Nov 5. [PubMed:33545852 ]
Song F, Xie T, Liu X, Chin B, Luo X, Liao S, Feng W, He M, Huang N, Su Z, Liu Y: UPLC/Q-TOF-MS-based Metabolomics Study of the Antiosteoporosis Effects of Vaccarin in Ovariectomized Mice. Planta Med. 2023 Feb;89(2):218-230. doi: 10.1055/a-1942-5428. Epub 2022 Sep 13. [PubMed:36100252 ]
Hou B, Wen Y, Zhu X, Qi M, Cai W, Du B, Sun H, Qiu L: Preparation and characterization of vaccarin, hypaphorine and chitosan nanoparticles and their promoting effects on chronic wounds healing. Int J Biol Macromol. 2022 Nov 30;221:1580-1592. doi: 10.1016/j.ijbiomac.2022.08.041. Epub 2022 Aug 10. [PubMed:35961560 ]
LOTUS database [Link]

Showing NP-Card for 6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one (NP0264960)

MOL for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

3D MOL for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

3D SDF for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

3D-SDF for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

PDB for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

3D PDB for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

SMILES for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

INCHI for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

Structure for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)

3D Structure for NP0264960 (6-[(3r,4s,5s,6r)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]-5,7-dihydroxy-2-(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)chromen-4-one)