NP-MRD: Showing NP-Card for (2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate (NP0251101)

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Record Information

Version

2.0

Created at

2022-09-07 14:11:28 UTC

Updated at

2022-09-07 14:11:28 UTC

NP-MRD ID

NP0251101

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate

Description

3'-O-benzoylmangiferin 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,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate is found in Fridericia patellifera. (2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate was first documented in 2008 (PMID: 18950229). Based on a literature review very few articles have been published on 3'-O-benzoylmangiferin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072216112D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309072216112D          

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  7 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
  4 32  1  0  0  0  0
 32 33  1  1  0  0  0
  2 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 34 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0251101

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=C(O)C=C3OC4=CC(O)=C(O)C=C4C(=O)C3=C2O)[C@H](O)[C@@H](OC(=O)C2=CC=CC=C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H22O13/c27-9-17-20(32)24(38-25(35)10-4-2-1-3-5-10)22(34)26(37-17)39-23-14(30)8-16-18(21(23)33)19(31)11-6-12(28)13(29)7-15(11)36-16/h1-8,17,20,22,24,26-30,32-34H,9H2/t17-,20-,22-,24+,26+/m1/s1

> <INCHI_KEY>
ANXOKJLEMDMTQX-FVFNWFHBSA-N

> <FORMULA>
C26H22O13

> <MOLECULAR_WEIGHT>
542.449

> <EXACT_MASS>
542.106040768

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
52.05454881208398

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxy]oxan-4-yl benzoate

> <JCHEM_LOGP>
2.3190453673333336

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.09231528354001

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.3952486508690995

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981111847968556

> <JCHEM_POLAR_SURFACE_AREA>
212.67

> <JCHEM_REFRACTIVITY>
128.6872

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       0.000 -12.320   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -1.334 -10.010   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.334 -11.550   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -2.667 -13.860   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -4.001 -14.630   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   32                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   28                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   26                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   25                                                  
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   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   15   23                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   13   26                                                  
CONECT   26   25    9   27                                                  
CONECT   27   26                                                            
CONECT   28    7   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29    4   33                                                  
CONECT   33   32                                                            
CONECT   34    2   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   34                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₂O₁₃

Average Mass

542.4490 Da

Monoisotopic Mass

542.10604 Da

IUPAC Name

(2R,3R,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxo-9H-xanthen-2-yl)oxy]oxan-4-yl benzoate

Traditional Name

(2R,3R,4S,5R,6S)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=C(O)C=C3OC4=CC(O)=C(O)C=C4C(=O)C3=C2O)[C@H](O)[C@@H](OC(=O)C2=CC=CC=C2)[C@@H]1O

InChI Identifier

InChI=1S/C26H22O13/c27-9-17-20(32)24(38-25(35)10-4-2-1-3-5-10)22(34)26(37-17)39-23-14(30)8-16-18(21(23)33)19(31)11-6-12(28)13(29)7-15(11)36-16/h1-8,17,20,22,24,26-30,32-34H,9H2/t17-,20-,22-,24+,26+/m1/s1

InChI Key

ANXOKJLEMDMTQX-FVFNWFHBSA-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
O-glycosyl compound
Glycosyl compound
Chromone
Benzoate ester
Benzoic acid or derivatives
Benzoyl
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Monosaccharide
Monocyclic benzene moiety
Oxane
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Carboxylic acid ester
Secondary alcohol
Acetal
Oxacycle
Carboxylic acid derivative
Polyol
Monocarboxylic acid or derivatives
Alcohol
Hydrocarbon derivative
Primary alcohol
Organic oxygen compound
Organooxygen compound
Organic oxide
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	2.32	ChemAxon
pKa (Strongest Acidic)	7.4	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	212.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	128.69 m³·mol⁻¹	ChemAxon
Polarizability	52.05 Å³	ChemAxon
Number of Rings	5	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

24636764

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45481966

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Martin F, Hay AE, Cressend D, Reist M, Vivas L, Gupta MP, Carrupt PA, Hostettmann K: Antioxidant C-glucosylxanthones from the leaves of Arrabidaea patellifera. J Nat Prod. 2008 Nov;71(11):1887-90. doi: 10.1021/np800406q. Epub 2008 Oct 25. [PubMed:18950229 ]
LOTUS database [Link]

Showing NP-Card for (2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate (NP0251101)

MOL for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

3D MOL for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

3D SDF for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

3D-SDF for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

PDB for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

3D PDB for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

SMILES for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

INCHI for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

Structure for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)

3D Structure for NP0251101 ((2r,3r,4s,5r,6s)-3,5-dihydroxy-2-(hydroxymethyl)-6-[(1,3,6,7-tetrahydroxy-9-oxoxanthen-2-yl)oxy]oxan-4-yl benzoate)