NP-MRD: Showing NP-Card for Swertiajaponin 3'-O-glucoside (NP0054156)

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Record Information

Version

1.0

Created at

2022-04-28 00:36:00 UTC

Updated at

2022-04-28 00:36:00 UTC

NP-MRD ID

NP0054156

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Swertiajaponin 3'-O-glucoside

Description

Swertiajaponin 3'-o-glucoside 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. Thus, swertiajaponin 3'-O-glucoside is considered to be a flavonoid. Swertiajaponin 3'-O-glucoside is found in Phragmites australis . Based on a literature review very few articles have been published on Swertiajaponin 3'-o-glucoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282202362D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282202362D          

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    6.4302   -1.2375    0.0000 O   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
    0.0000   -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  1  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
   -2.1434   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  2  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
   -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 O   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
   -2.1434   -3.7125    0.0000 O   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
   -1.4289    0.0000    0.0000 O   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
  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
  1  6  1  0  0  0  0
  5  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
  4 10  1  0  0  0  0
 10 11  2  0  0  0  0
  8 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 16 18  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 19 24  1  0  0  0  0
 23 25  1  6  0  0  0
 25 26  1  0  0  0  0
 22 27  1  1  0  0  0
 21 28  1  6  0  0  0
 20 29  1  1  0  0  0
 15 30  1  0  0  0  0
  3 31  1  0  0  0  0
 32  2  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 32 37  1  0  0  0  0
 36 38  1  1  0  0  0
 38 39  1  0  0  0  0
 35 40  1  6  0  0  0
 34 41  1  1  0  0  0
 33 42  1  6  0  0  0
  1 43  1  0  0  0  0
 43 44  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0054156

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(O)=C2C(=O)C=C(OC2=C1)C1=CC=C(O)C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O16/c1-40-14-6-15-18(22(35)19(14)27-25(38)23(36)20(33)16(7-29)42-27)11(32)5-12(41-15)9-2-3-10(31)13(4-9)43-28-26(39)24(37)21(34)17(8-30)44-28/h2-6,16-17,20-21,23-31,33-39H,7-8H2,1H3/t16-,17-,20-,21-,23+,24+,25-,26-,27+,28-/m1/s1

> <INCHI_KEY>
RXCSLWWSSDJODS-JFECCKQBSA-N

> <FORMULA>
C28H32O16

> <MOLECULAR_WEIGHT>
624.548

> <EXACT_MASS>
624.16903495

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
61.24040220970171

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.73

> <JCHEM_LOGP>
-2.476371130333333

> <ALOGPS_LOGS>
-2.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.051131663206371

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.929349537880507

> <JCHEM_PKA_STRONGEST_BASIC>
-3.644730893137912

> <JCHEM_POLAR_SURFACE_AREA>
265.52

> <JCHEM_REFRACTIVITY>
144.63979999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.57e+00 g/l

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

> <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      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6   43                                                  
CONECT    2    1    3   32                                                  
CONECT    3    2    4   31                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   30                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   29                                                  
CONECT   21   20   22   28                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23   19                                                       
CONECT   25   23   26                                                       
CONECT   26   25                                                            
CONECT   27   22                                                            
CONECT   28   21                                                            
CONECT   29   20                                                            
CONECT   30   15                                                            
CONECT   31    3                                                            
CONECT   32    2   33   37                                                  
CONECT   33   32   34   42                                                  
CONECT   34   33   35   41                                                  
CONECT   35   34   36   40                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36   32                                                       
CONECT   38   36   39                                                       
CONECT   39   38                                                            
CONECT   40   35                                                            
CONECT   41   34                                                            
CONECT   42   33                                                            
CONECT   43    1   44                                                       
CONECT   44   43                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   96    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₂O₁₆

Average Mass

624.5480 Da

Monoisotopic Mass

624.16903 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

COC1=C([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(O)=C2C(=O)C=C(OC2=C1)C1=CC=C(O)C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C1

InChI Identifier

InChI=1S/C28H32O16/c1-40-14-6-15-18(22(35)19(14)27-25(38)23(36)20(33)16(7-29)42-27)11(32)5-12(41-15)9-2-3-10(31)13(4-9)43-28-26(39)24(37)21(34)17(8-30)44-28/h2-6,16-17,20-21,23-31,33-39H,7-8H2,1H3/t16-,17-,20-,21-,23+,24+,25-,26-,27+,28-/m1/s1

InChI Key

RXCSLWWSSDJODS-JFECCKQBSA-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
Phragmites australis	Plant	KNApSAcK

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-3p-o-glycoside
Flavonoid o-glycoside
Flavonoid c-glycoside
7-methoxyflavonoid-skeleton
Hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Flavone
Phenolic glycoside
Glycosyl compound
O-glycosyl compound
Chromone
C-glycosyl compound
1-benzopyran
Benzopyran
Phenoxy compound
Anisole
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Phenol
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
Pyran
Oxane
Monosaccharide
Benzenoid
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Ether
Dialkyl ether
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Primary alcohol
Organic oxide
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen 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	-0.73	ALOGPS
logP	-2.5	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	6.93	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	265.52 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	144.64 m³·mol⁻¹	ChemAxon
Polarizability	61.24 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

C00006260

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

102153823

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Swertiajaponin 3'-O-glucoside (NP0054156)

MOL for NP0054156 (Swertiajaponin 3'-O-glucoside)

3D MOL for NP0054156 (Swertiajaponin 3'-O-glucoside)

3D SDF for NP0054156 (Swertiajaponin 3'-O-glucoside)

3D-SDF for NP0054156 (Swertiajaponin 3'-O-glucoside)

PDB for NP0054156 (Swertiajaponin 3'-O-glucoside)

3D PDB for NP0054156 (Swertiajaponin 3'-O-glucoside)

SMILES for NP0054156 (Swertiajaponin 3'-O-glucoside)

INCHI for NP0054156 (Swertiajaponin 3'-O-glucoside)

Structure for NP0054156 (Swertiajaponin 3'-O-glucoside)

3D Structure for NP0054156 (Swertiajaponin 3'-O-glucoside)