NP-MRD: Showing NP-Card for (3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one (NP0186625)

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Record Information

Version

2.0

Created at

2022-09-04 02:32:48 UTC

Updated at

2022-09-04 02:32:49 UTC

NP-MRD ID

NP0186625

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one

Description

(3E,4R)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methylidene]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. Based on a literature review very few articles have been published on (3E,4R)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042204322D          

 38 42  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309042204322D          

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 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 21 30  1  0  0  0  0
 30 31  1  1  0  0  0
 18 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 17 34  1  0  0  0  0
  5 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
  3 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0186625

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(C[C@H]2COC(=O)\C2=C\C2=CC=C3OCOC3=C2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O12/c1-33-18-7-12(2-4-16(18)28)6-14-10-34-25(32)15(14)8-13-3-5-17-24(36-11-35-17)23(13)38-26-22(31)21(30)20(29)19(9-27)37-26/h2-5,7-8,14,19-22,26-31H,6,9-11H2,1H3/b15-8+/t14-,19+,20+,21-,22+,26-/m0/s1

> <INCHI_KEY>
IZGWCAIZMZTEIB-CSGWIZRMSA-N

> <FORMULA>
C26H28O12

> <MOLECULAR_WEIGHT>
532.498

> <EXACT_MASS>
532.158076342

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
49.90192179158174

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
0.9710401849999994

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.202151586099337

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.943229855834662

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923574606676

> <JCHEM_POLAR_SURFACE_AREA>
173.6

> <JCHEM_REFRACTIVITY>
127.95840000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3E,4R)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0       6.613  -5.529   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.293  -4.023   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.437  -2.992   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.117  -1.486   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.262  -0.456   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.941   1.051   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.086   2.081   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.592   1.761   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      11.362   3.095   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.332   4.239   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.652   5.746   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       8.925   3.613   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.591   4.383   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.924   5.923   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       3.590   6.693   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.257   5.923   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       0.923   6.693   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.411   5.923   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.411   4.383   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.923   8.233   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.411   9.003   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.257   9.003   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.257  10.543   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.590   8.233   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.924   9.003   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       2.126   4.089   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.126   1.597   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       9.726  -0.931   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.046  -2.438   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.902  -3.468   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       9.222  -4.975   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   35                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    7   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   34                                                  
CONECT   18   17   19   32                                                  
CONECT   19   18   14   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   21   31                                                  
CONECT   31   30                                                            
CONECT   32   18   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   17                                                       
CONECT   35    5   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36    3   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₂

Average Mass

532.4980 Da

Monoisotopic Mass

532.15808 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

COC1=CC(C[C@H]2COC(=O)\C2=C\C2=CC=C3OCOC3=C2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=CC=C1O

InChI Identifier

InChI=1S/C26H28O12/c1-33-18-7-12(2-4-16(18)28)6-14-10-34-25(32)15(14)8-13-3-5-17-24(36-11-35-17)23(13)38-26-22(31)21(30)20(29)19(9-27)37-26/h2-5,7-8,14,19-22,26-31H,6,9-11H2,1H3/b15-8+/t14-,19+,20+,21-,22+,26-/m0/s1

InChI Key

IZGWCAIZMZTEIB-CSGWIZRMSA-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 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
Furanoid lignan
Lignan lactone
Phenolic glycoside
Glycosyl compound
O-glycosyl compound
Methoxyphenol
Benzodioxole
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monocyclic benzene moiety
Gamma butyrolactone
Benzenoid
Monosaccharide
Oxane
Tetrahydrofuran
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Secondary alcohol
Carboxylic acid ester
Lactone
Polyol
Acetal
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Ether
Organoheterocyclic compound
Carbonyl group
Organic oxide
Organooxygen compound
Primary alcohol
Alcohol
Hydrocarbon derivative
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	0.97	ChemAxon
pKa (Strongest Acidic)	9.94	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	127.96 m³·mol⁻¹	ChemAxon
Polarizability	49.9 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

163186476

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one (NP0186625)

MOL for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

3D MOL for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

3D SDF for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

3D-SDF for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

PDB for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

3D PDB for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

SMILES for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

INCHI for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

Structure for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)

3D Structure for NP0186625 ((3e,4r)-4-[(4-hydroxy-3-methoxyphenyl)methyl]-3-[(4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2h-1,3-benzodioxol-5-yl)methylidene]oxolan-2-one)