NP-MRD: Showing NP-Card for (2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0329778)

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Record Information

Version

2.0

Created at

2022-09-12 14:29:40 UTC

Updated at

2022-09-12 14:29:40 UTC

NP-MRD ID

NP0329778

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Description

(2S,3R,4S,5S,6R)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol 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. (2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol is found in Epimedium grandiflorum, Ligustrum obtusifolium, Sambucus racemosa and Saussurea costus. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122216292D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309122216292D          

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    5.7598   -5.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2448   -6.0504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9092   -6.8041    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3941   -7.4715    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 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
 17 16  1  6  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  6  0  0  0
 20 21  1  0  0  0  0
 19 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 17 26  1  0  0  0  0
 26 27  1  1  0  0  0
 15 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 28 31  2  0  0  0  0
 12 31  1  0  0  0  0
  9 32  1  0  0  0  0
  6 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 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>
NP0329778

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1O)C1OCC(O)(CC2=CC=C(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C(OC)=C2)C1CO

> <INCHI_IDENTIFIER>
InChI=1S/C26H34O12/c1-34-18-8-14(4-5-16(18)29)24-15(10-27)26(33,12-36-24)9-13-3-6-17(19(7-13)35-2)37-25-23(32)22(31)21(30)20(11-28)38-25/h3-8,15,20-25,27-33H,9-12H2,1-2H3/t15?,20-,21-,22+,23-,24?,25-,26?/m1/s1

> <INCHI_KEY>
SXGSYHDLSPXCMU-DULKRDRMSA-N

> <FORMULA>
C26H34O12

> <MOLECULAR_WEIGHT>
538.546

> <EXACT_MASS>
538.205026535

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
53.55278277261213

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4S,5S,6R)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_LOGP>
-0.7830246623333335

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.18094087808925

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.908332113039348

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6753338846636128

> <JCHEM_POLAR_SURFACE_AREA>
187.76

> <JCHEM_REFRACTIVITY>
130.42830000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4S,5S,6R)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0       9.778 -15.515   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       8.873 -14.269   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       9.499 -12.862   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.594 -11.616   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.220 -10.209   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.315  -8.963   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.775  -8.963   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.299  -7.499   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.545  -6.594   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.514  -5.449   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.575  -5.449   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.100  -3.984   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       9.130  -2.840   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.654  -1.375   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.148  -1.055   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.672   0.409   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.702   1.554   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.226   3.019   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.257   4.163   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.781   5.628   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       6.275   5.948   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       9.763   3.843   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.794   4.987   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      10.239   2.378   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      11.745   2.058   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       9.209   1.234   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.685  -0.231   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       6.117  -2.200   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       4.611  -1.879   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       3.580  -3.024   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.593  -3.664   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.791  -7.499   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      10.255  -7.023   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      11.400  -8.053   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      10.752 -10.048   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      11.657 -11.294   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      11.031 -12.701   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      11.936 -13.947   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   32                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   32                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   28                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   26                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   17   27                                                  
CONECT   27   26                                                            
CONECT   28   15   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   12                                                       
CONECT   32    9    6   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
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   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₄O₁₂

Average Mass

538.5460 Da

Monoisotopic Mass

538.20503 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1O)C1OCC(O)(CC2=CC=C(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)C(OC)=C2)C1CO

InChI Identifier

InChI=1S/C26H34O12/c1-34-18-8-14(4-5-16(18)29)24-15(10-27)26(33,12-36-24)9-13-3-6-17(19(7-13)35-2)37-25-23(32)22(31)21(30)20(11-28)38-25/h3-8,15,20-25,27-33H,9-12H2,1-2H3/t15?,20-,21-,22+,23-,24?,25-,26?/m1/s1

InChI Key

SXGSYHDLSPXCMU-DULKRDRMSA-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
Epimedium grandiflorum	LOTUS Database	35616633
Ligustrum obtusifolium	LOTUS Database	35616633
Sambucus racemosa	LOTUS Database	35616633
Saussurea costus	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
Tetrahydrofuran lignan
7,9p-epoxylignan
Furanoid lignan
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Phenolic glycoside
Alkyl glycoside
O-glycosyl compound
Glycosyl compound
Methoxyphenol
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxane
Fatty acyl
Benzenoid
Monosaccharide
Monocyclic benzene moiety
Tertiary alcohol
Oxolane
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Dialkyl ether
Ether
Acetal
Hydrocarbon derivative
Organic oxygen compound
Primary alcohol
Alcohol
Organooxygen compound
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	-0.78	ChemAxon
pKa (Strongest Acidic)	9.91	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	187.76 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	130.43 m³·mol⁻¹	ChemAxon
Polarizability	53.55 Å³	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

5320285

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0329778)

MOL for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0329778 ((2s,3r,4s,5s,6r)-2-(4-{[3-hydroxy-5-(4-hydroxy-3-methoxyphenyl)-4-(hydroxymethyl)oxolan-3-yl]methyl}-2-methoxyphenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)