NP-MRD: Showing NP-Card for [(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate (NP0328400)

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Record Information

Version

2.0

Created at

2022-09-12 11:50:30 UTC

Updated at

2022-09-12 11:50:31 UTC

NP-MRD ID

NP0328400

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate

Description

[(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate 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)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate is found in Melaleuca leucadendra. Based on a literature review very few articles have been published on [(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122213502D          

 40 43  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309122213502D          

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  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
 15 22  1  0  0  0  0
 12 23  1  0  0  0  0
 23 24  2  0  0  0  0
  9 24  1  0  0  0  0
 24 25  1  0  0  0  0
  7 26  1  0  0  0  0
 26 27  1  6  0  0  0
 26 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
  5 30  1  0  0  0  0
 30 31  1  6  0  0  0
  2 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  2  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 38 39  1  0  0  0  0
 38 40  2  0  0  0  0
 32 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0328400

> <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=C(\C=C\C3=CC(O)=CC(O)=C3)C=C2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H26O13/c28-15-5-13(6-16(29)10-15)2-1-12-3-4-20(17(30)7-12)39-27-25(36)24(35)23(34)21(40-27)11-38-26(37)14-8-18(31)22(33)19(32)9-14/h1-10,21,23-25,27-36H,11H2/b2-1+/t21-,23-,24+,25-,27-/m1/s1

> <INCHI_KEY>
WBKDRBRGYHZWCT-XMPPFBFMSA-N

> <FORMULA>
C27H26O13

> <MOLECULAR_WEIGHT>
558.492

> <EXACT_MASS>
558.137340897

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
54.70007131954689

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate

> <JCHEM_LOGP>
2.415361355

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.64965758593676

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.9726948384891845

> <JCHEM_PKA_STRONGEST_BASIC>
-3.678967020864805

> <JCHEM_POLAR_SURFACE_AREA>
226.82999999999998

> <JCHEM_REFRACTIVITY>
137.34550000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate

> <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  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       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002 -13.860   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668 -14.630   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668 -16.170   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002 -16.940   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002 -18.480   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336 -19.250   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       6.668 -19.250   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335 -18.480   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.001 -19.250   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       5.335 -16.940   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      10.669  -9.240   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.335  -9.240   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   32                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   30                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   26                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   24                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   23                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15                                                       
CONECT   23   12   24                                                       
CONECT   24   23    9   25                                                  
CONECT   25   24                                                            
CONECT   26    7   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28    5   31                                                  
CONECT   31   30                                                            
CONECT   32    2   33   40                                                  
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   32                                                       
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Value	Source
[(2R,3S,4S,5R,6S)-6-{4-[(e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoic acid	Generator

Chemical Formula

C₂₇H₂₆O₁₃

Average Mass

558.4920 Da

Monoisotopic Mass

558.13734 Da

IUPAC Name

[(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate

Traditional Name

[(2R,3S,4S,5R,6S)-6-{4-[(E)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-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=C(\C=C\C3=CC(O)=CC(O)=C3)C=C2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C27H26O13/c28-15-5-13(6-16(29)10-15)2-1-12-3-4-20(17(30)7-12)39-27-25(36)24(35)23(34)21(40-27)11-38-26(37)14-8-18(31)22(33)19(32)9-14/h1-10,21,23-25,27-36H,11H2/b2-1+/t21-,23-,24+,25-,27-/m1/s1

InChI Key

WBKDRBRGYHZWCT-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
Melaleuca leucadendra	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
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Galloyl ester
Alkyl glycoside
Gallic acid or derivatives
O-glycosyl compound
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Glycosyl compound
Benzoate ester
Pyrogallol derivative
Benzenetriol
Benzoic acid or derivatives
Phenoxy compound
Phenol ether
Resorcinol
Styrene
Benzoyl
Phenol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Monosaccharide
Oxane
Secondary alcohol
Carboxylic acid ester
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Polyol
Monocarboxylic acid or derivatives
Acetal
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organic oxide
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	2.42	ChemAxon
pKa (Strongest Acidic)	7.97	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	226.83 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	137.35 m³·mol⁻¹	ChemAxon
Polarizability	54.7 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

10258881

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14077412

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)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate (NP0328400)

MOL for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D MOL for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D SDF for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D-SDF for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

PDB for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D PDB for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

SMILES for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

INCHI for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

Structure for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)

3D Structure for NP0328400 ([(2r,3s,4s,5r,6s)-6-{4-[(1e)-2-(3,5-dihydroxyphenyl)ethenyl]-2-hydroxyphenoxy}-3,4,5-trihydroxyoxan-2-yl]methyl 3,4,5-trihydroxybenzoate)