NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol (NP0215700)

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Record Information

Version

2.0

Created at

2022-09-05 15:24:25 UTC

Updated at

2022-09-05 15:24:25 UTC

NP-MRD ID

NP0215700

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol

Description

Toricornoside A belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol is found in Polygala karensium. Based on a literature review very few articles have been published on Toricornoside A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052217242D          

 37 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052217242D          

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 32 33  1  1  0  0  0
 32 34  1  6  0  0  0
 34 35  1  0  0  0  0
 32 36  1  0  0  0  0
 29 36  1  0  0  0  0
 36 37  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0215700

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC(O)=CC(O)=C2C(=O)C2=CC=CC=C2)[C@H](O[C@@H]2OC[C@](O)(CO)[C@H]2O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O13/c25-8-15-18(30)19(31)20(37-23-21(32)24(33,9-26)10-34-23)22(36-15)35-14-7-12(27)6-13(28)16(14)17(29)11-4-2-1-3-5-11/h1-7,15,18-23,25-28,30-33H,8-10H2/t15-,18-,19+,20-,21+,22-,23+,24-/m1/s1

> <INCHI_KEY>
GNZXMFPBYJMTPZ-OZYQASBSSA-N

> <FORMULA>
C24H28O13

> <MOLECULAR_WEIGHT>
524.475

> <EXACT_MASS>
524.152990962

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
50.529791479015216

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6S)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol

> <JCHEM_LOGP>
-0.3726642650000001

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.72916477711173

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.1189313026029915

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810925718905663

> <JCHEM_POLAR_SURFACE_AREA>
215.82999999999996

> <JCHEM_REFRACTIVITY>
121.39080000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6S)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol

> <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  O   UNK     0      12.113  -2.575   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      13.018  -3.821   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.549  -3.660   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.176  -2.253   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.707  -2.092   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.613  -3.338   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      16.986  -4.744   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.455  -4.905   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.392  -5.227   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.297  -6.473   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      14.828  -6.312   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.670  -7.880   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.139  -8.041   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      10.512  -9.448   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.234  -6.795   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.860  -5.388   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.955  -4.142   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       8.423  -4.303   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       7.797  -5.710   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.265  -5.871   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.639  -7.278   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       4.107  -7.439   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.360  -4.625   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.829  -4.786   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.986  -3.219   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.081  -1.973   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.518  -3.058   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       8.144  -1.651   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       7.239  -0.405   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.699  -0.405   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.223   1.060   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.469   1.965   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.439   3.109   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       7.500   3.109   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.024   4.574   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       7.715   1.060   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.180   1.536   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    2   10   16                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15    9   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   18   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   36                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   34   36                                             
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34                                                            
CONECT   36   32   29   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₈O₁₃

Average Mass

524.4750 Da

Monoisotopic Mass

524.15299 Da

IUPAC Name

(2R,3S,4S,5R,6S)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol

Traditional Name

(2R,3S,4S,5R,6S)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC(O)=CC(O)=C2C(=O)C2=CC=CC=C2)[C@H](O[C@@H]2OC[C@](O)(CO)[C@H]2O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C24H28O13/c25-8-15-18(30)19(31)20(37-23-21(32)24(33,9-26)10-34-23)22(36-15)35-14-7-12(27)6-13(28)16(14)17(29)11-4-2-1-3-5-11/h1-7,15,18-23,25-28,30-33H,8-10H2/t15-,18-,19+,20-,21+,22-,23+,24-/m1/s1

InChI Key

GNZXMFPBYJMTPZ-OZYQASBSSA-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 karensium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Benzophenone
Diphenylmethane
Aryl-phenylketone
O-glycosyl compound
Disaccharide
Phenoxy compound
Phenol ether
Resorcinol
Aryl ketone
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
Phenol
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Oxane
Monocyclic benzene moiety
Tertiary alcohol
Oxolane
Vinylogous acid
Secondary alcohol
Ketone
Acetal
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Alcohol
Aldehyde
Primary alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	-0.37	ChemAxon
pKa (Strongest Acidic)	7.12	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	215.83 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	121.39 m³·mol⁻¹	ChemAxon
Polarizability	50.53 Å³	ChemAxon
Number of Rings	4	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

9744738

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11569968

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol (NP0215700)

MOL for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

3D MOL for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

3D SDF for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

3D-SDF for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

PDB for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

3D PDB for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

SMILES for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

INCHI for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

Structure for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)

3D Structure for NP0215700 ((2r,3s,4s,5r,6s)-6-(2-benzoyl-3,5-dihydroxyphenoxy)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)oxane-3,4-diol)