NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol (NP0189536)

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Record Information

Version

2.0

Created at

2022-09-04 06:02:00 UTC

Updated at

2022-09-04 06:02:00 UTC

NP-MRD ID

NP0189536

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol

Description

(2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol 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,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol is found in Polygala tenuifolia. Based on a literature review very few articles have been published on (2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042208022D          

 35 37  0  0  1  0            999 V2000
    6.4890   -1.3793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2726   -4.8889    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0931   -4.8027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309042208022D          

 35 37  0  0  1  0            999 V2000
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 16 25  1  0  0  0  0
 25 26  1  1  0  0  0
 27 26  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  6  0  0  0
 32 33  1  0  0  0  0
 30 34  1  0  0  0  0
 27 34  1  0  0  0  0
 34 35  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0189536

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(\C=C/CO)=CC(OC)=C1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O[C@@H]1OC[C@](O)(CO)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C22H32O13/c1-30-12-6-11(4-3-5-23)7-13(31-2)17(12)34-20-18(16(27)15(26)14(8-24)33-20)35-21-19(28)22(29,9-25)10-32-21/h3-4,6-7,14-16,18-21,23-29H,5,8-10H2,1-2H3/b4-3-/t14-,15-,16+,18-,19+,20-,21+,22-/m1/s1

> <INCHI_KEY>
NFIMXUUPAACHLN-PASLCOJCSA-N

> <FORMULA>
C22H32O13

> <MOLECULAR_WEIGHT>
504.485

> <EXACT_MASS>
504.18429109

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
49.620418828217026

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol

> <JCHEM_LOGP>
-2.3476632843333345

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.6516982843907

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.807495375883864

> <JCHEM_PKA_STRONGEST_BASIC>
-2.526500400525862

> <JCHEM_POLAR_SURFACE_AREA>
196.98999999999998

> <JCHEM_REFRACTIVITY>
116.91440000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol

> <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      12.113  -2.575   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      13.018  -3.821   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      12.392  -5.227   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.297  -6.473   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.670  -7.880   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.576  -9.126   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      15.107  -8.965   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.733  -7.558   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      17.265  -7.397   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      11.139  -8.041   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.234  -6.795   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       8.702  -6.956   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.076  -8.363   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.860  -5.388   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       9.955  -4.142   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.423  -4.303   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.797  -5.710   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.265  -5.871   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.639  -7.278   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.107  -7.439   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.360  -4.625   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       3.829  -4.786   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.986  -3.219   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.081  -1.973   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       7.518  -3.058   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       8.144  -1.651   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.239  -0.405   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.699  -0.405   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.223   1.060   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.469   1.965   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       5.439   3.109   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       7.500   3.109   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       7.024   4.574   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       7.715   1.060   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.180   1.536   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8                                                            
CONECT   10    5   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11    3   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   16   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32   34                                             
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32                                                            
CONECT   34   30   27   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₃₂O₁₃

Average Mass

504.4850 Da

Monoisotopic Mass

504.18429 Da

IUPAC Name

(2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol

Traditional Name

(2R,3S,4S,5R,6R)-5-{[(2S,3R,4R)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1Z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol

CAS Registry Number

Not Available

SMILES

COC1=CC(\C=C/CO)=CC(OC)=C1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O[C@@H]1OC[C@](O)(CO)[C@H]1O

InChI Identifier

InChI=1S/C22H32O13/c1-30-12-6-11(4-3-5-23)7-13(31-2)17(12)34-20-18(16(27)15(26)14(8-24)33-20)35-21-19(28)22(29,9-25)10-32-21/h3-4,6-7,14-16,18-21,23-29H,5,8-10H2,1-2H3/b4-3-/t14-,15-,16+,18-,19+,20-,21+,22-/m1/s1

InChI Key

NFIMXUUPAACHLN-PASLCOJCSA-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 tenuifolia	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
Disaccharide
O-glycosyl compound
Cinnamyl alcohol
Dimethoxybenzene
M-dimethoxybenzene
Methoxybenzene
Anisole
Phenoxy compound
Phenol ether
Styrene
Alkyl aryl ether
Benzenoid
Monocyclic benzene moiety
Oxane
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Organoheterocyclic compound
Ether
Acetal
Oxacycle
Hydrocarbon derivative
Alcohol
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	-2.3	ChemAxon
pKa (Strongest Acidic)	11.81	ChemAxon
pKa (Strongest Basic)	-2.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	196.99 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	116.91 m³·mol⁻¹	ChemAxon
Polarizability	49.62 Å³	ChemAxon
Number of Rings	3	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

163185590

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,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol (NP0189536)

MOL for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

3D MOL for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

3D SDF for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

3D-SDF for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

PDB for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

3D PDB for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

SMILES for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

INCHI for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

Structure for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)

3D Structure for NP0189536 ((2r,3s,4s,5r,6r)-5-{[(2s,3r,4r)-3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-2-(hydroxymethyl)-6-{4-[(1z)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenoxy}oxane-3,4-diol)