NP-MRD: Showing NP-Card for 4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one (NP0181555)

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Record Information

Version

2.0

Created at

2022-09-03 20:05:42 UTC

Updated at

2022-09-03 20:05:42 UTC

NP-MRD ID

NP0181555

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one

Description

4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones. 4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one is found in Schisandra rubriflora. 4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241501462D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004241501462D          

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 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 27 28  2  0  0  0  0
 20 28  1  0  0  0  0
 18 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 17 31  1  0  0  0  0
 31 32  2  0  0  0  0
  5 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
  3 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0181555

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC3=C(OCO3)C=C2CC2C(CC3=CC=C4OCOC4=C3)COC2=O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O12/c27-8-21-22(28)23(29)24(30)26(38-21)37-17-7-20-19(35-11-36-20)6-13(17)5-15-14(9-32-25(15)31)3-12-1-2-16-18(4-12)34-10-33-16/h1-2,4,6-7,14-15,21-24,26-30H,3,5,8-11H2

> <INCHI_KEY>
NAGPHNGRNKMFGK-UHFFFAOYSA-N

> <FORMULA>
C26H28O12

> <MOLECULAR_WEIGHT>
532.498

> <EXACT_MASS>
532.158076342

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
52.39204146893751

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one

> <ALOGPS_LOGP>
0.75

> <JCHEM_LOGP>
0.889089205999999

> <ALOGPS_LOGS>
-2.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.196085767112763

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.200126659674766

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923448998814

> <JCHEM_POLAR_SURFACE_AREA>
162.60000000000002

> <JCHEM_REFRACTIVITY>
124.4053

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.27e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0      18.265   0.960   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      16.801   1.436   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.480   2.942   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      15.016   3.418   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      14.696   4.924   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      13.231   5.400   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      12.911   6.907   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      14.055   7.937   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.735   9.444   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      14.640  10.689   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.735  11.935   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.270  11.459   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      12.270   9.919   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.126   8.889   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.446   7.383   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.302   6.352   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.837   6.828   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.591   5.923   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.126   1.597   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.126   4.089   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.345   6.828   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       6.821   8.293   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       8.361   8.293   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       9.266   9.539   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      15.840   5.955   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      15.520   7.461   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      17.305   5.479   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      18.449   6.510   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      17.625   3.973   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      19.090   3.497   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   33                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14    7   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   31                                                  
CONECT   18   17   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   27                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   23   28                                                  
CONECT   28   27   20                                                       
CONECT   29   18   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   17   32                                                  
CONECT   32   31                                                            
CONECT   33    5   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35    3   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₂

Average Mass

532.4980 Da

Monoisotopic Mass

532.15808 Da

IUPAC Name

4-[(2H-1,3-benzodioxol-5-yl)methyl]-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one

Traditional Name

4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methyl]oxolan-2-one

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC3=C(OCO3)C=C2CC2C(CC3=CC=C4OCOC4=C3)COC2=O)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H28O12/c27-8-21-22(28)23(29)24(30)26(38-21)37-17-7-20-19(35-11-36-20)6-13(17)5-15-14(9-32-25(15)31)3-12-1-2-16-18(4-12)34-10-33-16/h1-2,4,6-7,14-15,21-24,26-30H,3,5,8-11H2

InChI Key

NAGPHNGRNKMFGK-UHFFFAOYSA-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
Schisandra rubriflora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
Dibenzylbutyrolactone
Lignan lactone
Furanoid lignan
9,9p-epoxylignan
Tetrahydrofuran lignan
Phenolic glycoside
Glycosyl compound
O-glycosyl compound
Benzodioxole
Gamma butyrolactone
Monosaccharide
Benzenoid
Oxane
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Polyol
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Alcohol
Carbonyl group
Primary alcohol
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	0.75	ALOGPS
logP	0.89	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	162.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	124.41 m³·mol⁻¹	ChemAxon
Polarizability	52.39 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

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one (NP0181555)

MOL for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

3D MOL for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

3D SDF for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

3D-SDF for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

PDB for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

3D PDB for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

SMILES for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

INCHI for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

Structure for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)

3D Structure for NP0181555 (4-(2h-1,3-benzodioxol-5-ylmethyl)-3-[(6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methyl]oxolan-2-one)