NP-MRD: Showing NP-Card for [(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0206041)

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Record Information

Version

2.0

Created at

2022-09-05 02:07:45 UTC

Updated at

2022-09-05 02:07:45 UTC

NP-MRD ID

NP0206041

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate

Description

2,3,6,8-Tetrahydroxy-7-[6-O-[(E)-4-hydroxycinnamoyl]-beta-D-glucopyranosyl]-9H-xanthene-9-one belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. [(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate is found in Fridericia patellifera. Based on a literature review very few articles have been published on 2,3,6,8-Tetrahydroxy-7-[6-O-[(E)-4-hydroxycinnamoyl]-beta-D-glucopyranosyl]-9H-xanthene-9-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052204072D          

 41 45  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052204072D          

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   -1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 11  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  1  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 21 33  1  0  0  0  0
 33 34  2  0  0  0  0
 17 34  1  0  0  0  0
 34 35  1  0  0  0  0
 16 36  1  0  0  0  0
 36 37  1  6  0  0  0
 36 38  1  0  0  0  0
 38 39  1  1  0  0  0
 38 40  1  0  0  0  0
 14 40  1  0  0  0  0
 40 41  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0206041

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1[C@@H](COC(=O)\C=C\C2=CC=C(O)C=C2)O[C@H]([C@H](O)[C@H]1O)C1=C(O)C=C2OC3=CC(O)=C(O)C=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H24O13/c29-12-4-1-11(2-5-12)3-6-20(33)39-10-19-24(35)26(37)27(38)28(41-19)21-16(32)9-18-22(25(21)36)23(34)13-7-14(30)15(31)8-17(13)40-18/h1-9,19,24,26-32,35-38H,10H2/b6-3+/t19-,24-,26+,27-,28+/m1/s1

> <INCHI_KEY>
LXKAQLICMWHHHN-QHVSNWRPSA-N

> <FORMULA>
C28H24O13

> <MOLECULAR_WEIGHT>
568.487

> <EXACT_MASS>
568.121690833

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
55.38159641535344

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
2.368383425

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.660226936666686

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.975709077125872

> <JCHEM_PKA_STRONGEST_BASIC>
-3.645445676187647

> <JCHEM_POLAR_SURFACE_AREA>
223.67

> <JCHEM_REFRACTIVITY>
139.4068

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -9.336 -10.010   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.669  -9.240   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0     -12.003 -10.010   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0     -10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10    5                                                       
CONECT   12    2   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   40                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   36                                                  
CONECT   17   16   18   34                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   33                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   23   31                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   21   34                                                  
CONECT   34   33   17   35                                                  
CONECT   35   34                                                            
CONECT   36   16   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   14   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Value	Source
2,3,6,8-Tetrahydroxy-7-[6-O-[(e)-4-hydroxycinnamoyl]-b-D-glucopyranosyl]-9H-xanthene-9-one	Generator
2,3,6,8-Tetrahydroxy-7-[6-O-[(e)-4-hydroxycinnamoyl]-β-D-glucopyranosyl]-9H-xanthene-9-one	Generator

Chemical Formula

C₂₈H₂₄O₁₃

Average Mass

568.4870 Da

Monoisotopic Mass

568.12169 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

O[C@@H]1[C@@H](COC(=O)\C=C\C2=CC=C(O)C=C2)O[C@H]([C@H](O)[C@H]1O)C1=C(O)C=C2OC3=CC(O)=C(O)C=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C28H24O13/c29-12-4-1-11(2-5-12)3-6-20(33)39-10-19-24(35)26(37)27(38)28(41-19)21-16(32)9-18-22(25(21)36)23(34)13-7-14(30)15(31)8-17(13)40-18/h1-9,19,24,26-32,35-38H,10H2/b6-3+/t19-,24-,26+,27-,28+/m1/s1

InChI Key

LXKAQLICMWHHHN-QHVSNWRPSA-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
Fridericia patellifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Phenolic glycoside
Xanthone
Coumaric acid ester
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hydroxycinnamic acid or derivatives
Cinnamic acid ester
C-glycosyl compound
Chromone
Glycosyl compound
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Fatty acid ester
Phenol
Pyranone
Pyran
Monocyclic benzene moiety
Oxane
Monosaccharide
Benzenoid
Fatty acyl
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Vinylogous acid
Heteroaromatic compound
Secondary alcohol
1,2-diol
Carboxylic acid ester
Polyol
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Ether
Dialkyl ether
Organooxygen compound
Alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Carbonyl group
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	2.37	ChemAxon
pKa (Strongest Acidic)	6.98	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	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

25156147

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,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0206041)

MOL for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D MOL for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D SDF for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D-SDF for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

PDB for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D PDB for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

SMILES for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

INCHI for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

Structure for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D Structure for NP0206041 ([(2r,3s,4r,5r,6s)-3,4,5-trihydroxy-6-(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxan-2-yl]methyl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)