NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate (NP0228889)

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Record Information

Version

2.0

Created at

2022-09-06 08:43:20 UTC

Updated at

2022-09-06 08:43:21 UTC

NP-MRD ID

NP0228889

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate

Description

CHEMBL480304, also known as RGGP CPD, belongs to the class of organic compounds known as stilbene glycosides. Stilbene glycosides are compounds structurally characterized by the presence of a carbohydrate moiety glycosidically linked to the stilbene skeleton. [(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate is found in Fagopyrum megacarpum. Based on a literature review very few articles have been published on CHEMBL480304.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062210432D          

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M  END

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M  END


  Mrv1652309062210432D          

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  7 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
  5 29  1  0  0  0  0
 29 30  1  6  0  0  0
  2 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
 37 39  2  0  0  0  0
 31 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0228889

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COC(=O)C2=CC(O)=C(O)C(O)=C2)O[C@@H](OC2=CC(O)=CC(\C=C\C3=CC=C(O)C=C3)=C2)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H26O12/c28-16-5-3-13(4-6-16)1-2-14-7-17(29)11-18(8-14)38-27-25(35)24(34)23(33)21(39-27)12-37-26(36)15-9-19(30)22(32)20(31)10-15/h1-11,21,23-25,27-35H,12H2/b2-1+/t21-,23-,24+,25-,27-/m1/s1

> <INCHI_KEY>
YGKDMUYXJBMRBO-XMPPFBFMSA-N

> <FORMULA>
C27H26O12

> <MOLECULAR_WEIGHT>
542.493

> <EXACT_MASS>
542.142426277

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
53.169049472103

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(E)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate

> <JCHEM_LOGP>
2.718926676666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.689829704231984

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.987196941628415

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649110481414241

> <JCHEM_POLAR_SURFACE_AREA>
206.6

> <JCHEM_REFRACTIVITY>
135.36460000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(E)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.002  -7.700   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.669 -12.320   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001 -16.170   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667 -16.940   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334 -16.170   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.000 -16.940   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.334 -14.630   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   29                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   25                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   24                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   24                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   17                                                       
CONECT   24   14    9                                                       
CONECT   25    7   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27    5   30                                                  
CONECT   30   29                                                            
CONECT   31    2   32   39                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   31                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
RGGP CPD	MeSH
(e)-Resveratrol 3-(6''-galloyl)-O-beta-D-glucopyranoside	MeSH

Chemical Formula

C₂₇H₂₆O₁₂

Average Mass

542.4930 Da

Monoisotopic Mass

542.14243 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(E)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate

Traditional Name

[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(E)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COC(=O)C2=CC(O)=C(O)C(O)=C2)O[C@@H](OC2=CC(O)=CC(\C=C\C3=CC=C(O)C=C3)=C2)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C27H26O12/c28-16-5-3-13(4-6-16)1-2-14-7-17(29)11-18(8-14)38-27-25(35)24(34)23(33)21(39-27)12-37-26(36)15-9-19(30)22(32)20(31)10-15/h1-11,21,23-25,27-35H,12H2/b2-1+/t21-,23-,24+,25-,27-/m1/s1

InChI Key

YGKDMUYXJBMRBO-XMPPFBFMSA-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
Fagopyrum megacarpum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stilbene glycosides. Stilbene glycosides are compounds structurally characterized by the presence of a carbohydrate moiety glycosidically linked to the stilbene skeleton.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Stilbenes

Sub Class

Stilbene glycosides

Direct Parent

Stilbene glycosides

Alternative Parents

Substituents

Stilbene glycoside
Phenolic glycoside
Galloyl ester
Gallic acid or derivatives
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Glycosyl compound
O-glycosyl compound
Benzoate ester
Pyrogallol derivative
Benzenetriol
Benzoic acid or derivatives
Phenol ether
Phenoxy compound
Styrene
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
1-hydroxy-4-unsubstituted benzenoid
Monocyclic benzene moiety
Monosaccharide
Oxane
Benzenoid
Secondary alcohol
Carboxylic acid ester
Acetal
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Monocarboxylic acid or derivatives
Alcohol
Organic oxygen compound
Organic oxide
Organooxygen compound
Hydrocarbon derivative
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	2.72	ChemAxon
pKa (Strongest Acidic)	7.99	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	206.6 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	135.36 m³·mol⁻¹	ChemAxon
Polarizability	53.17 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

9505139

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11330189

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)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate (NP0228889)

MOL for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D MOL for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D SDF for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D-SDF for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

PDB for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D PDB for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

SMILES for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

INCHI for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

Structure for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D Structure for NP0228889 ([(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{3-hydroxy-5-[(1e)-2-(4-hydroxyphenyl)ethenyl]phenoxy}oxan-2-yl]methyl 3,4,5-trihydroxybenzoate)