NP-MRD: Showing NP-Card for 2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one (NP0329416)

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Record Information

Version

2.0

Created at

2022-09-12 13:46:12 UTC

Updated at

2022-09-12 13:46:12 UTC

NP-MRD ID

NP0329416

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one

Description

2-(3-{[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxy-9H-xanthen-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. 2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one is found in Polygala sibirica and Polygala tenuifolia. 2-(3-{[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxy-9H-xanthen-9-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004161501552D          

 38 42  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1533004161501552D          

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 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 27 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
 25 36  1  0  0  0  0
 36 37  2  0  0  0  0
 21 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0329416

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(C(OC2OCC(O)(CO)C2O)C(O)C1O)C1=C(O)C=C2OC3=CC=C(O)C=C3C(=O)C2=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H26O14/c25-5-13-17(30)19(32)21(38-23-22(33)24(34,6-26)7-35-23)20(37-13)14-10(28)4-12-15(18(14)31)16(29)9-3-8(27)1-2-11(9)36-12/h1-4,13,17,19-23,25-28,30-34H,5-7H2

> <INCHI_KEY>
LLMCZIBSELEBMK-UHFFFAOYSA-N

> <FORMULA>
C24H26O14

> <MOLECULAR_WEIGHT>
538.458

> <EXACT_MASS>
538.132255517

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
51.04753395025463

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-1.3348757096666672

> <ALOGPS_LOGS>
-1.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.575724959522297

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.1048367672735555

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423791325182915

> <JCHEM_POLAR_SURFACE_AREA>
236.05999999999995

> <JCHEM_REFRACTIVITY>
122.54749999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.46e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.421 -10.145   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.897 -11.610   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.437 -11.610   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.276 -13.141   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.944 -11.930   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.974 -10.786   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.913 -10.145   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.378  -9.669   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   15                                             
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13                                                            
CONECT   15   11    8   16                                                  
CONECT   16   15                                                            
CONECT   17    6   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17    3   20                                                  
CONECT   20   19                                                            
CONECT   21    5   22   37                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   36                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   27   34                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   25   37                                                  
CONECT   37   36   21   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆O₁₄

Average Mass

538.4580 Da

Monoisotopic Mass

538.13226 Da

IUPAC Name

2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxy-9H-xanthen-9-one

Traditional Name

2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one

CAS Registry Number

Not Available

SMILES

OCC1OC(C(OC2OCC(O)(CO)C2O)C(O)C1O)C1=C(O)C=C2OC3=CC=C(O)C=C3C(=O)C2=C1O

InChI Identifier

InChI=1S/C24H26O14/c25-5-13-17(30)19(32)21(38-23-22(33)24(34,6-26)7-35-23)20(37-13)14-10(28)4-12-15(18(14)31)16(29)9-3-8(27)1-2-11(9)36-12/h1-4,13,17,19-23,25-28,30-34H,5-7H2

InChI Key

LLMCZIBSELEBMK-UHFFFAOYSA-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 sibirica	LOTUS Database	35616633
Polygala tenuifolia	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
C-glycosyl compound
Chromone
Disaccharide
O-glycosyl compound
Glycosyl compound
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Oxane
Pyran
Benzenoid
Oxolane
Vinylogous acid
Tertiary alcohol
Heteroaromatic compound
Secondary alcohol
Acetal
Dialkyl ether
Ether
Oxacycle
Polyol
Hydrocarbon derivative
Alcohol
Organic oxygen compound
Primary alcohol
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	-0.59	ALOGPS
logP	-1.3	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	7.1	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	236.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	122.55 m³·mol⁻¹	ChemAxon
Polarizability	51.05 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	No	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

73804949

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one (NP0329416)

MOL for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

3D MOL for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

3D SDF for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

3D-SDF for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

PDB for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

3D PDB for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

SMILES for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

INCHI for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

Structure for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)

3D Structure for NP0329416 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,7-trihydroxyxanthen-9-one)