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)-1,3,6-trihydroxy-7-methoxyxanthen-9-one (NP0313287)

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Record Information

Version

2.0

Created at

2022-09-11 10:43:41 UTC

Updated at

2022-09-11 10:43:41 UTC

NP-MRD ID

NP0313287

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)-1,3,6-trihydroxy-7-methoxyxanthen-9-one

Description

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

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251505572D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251505572D          

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    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 26 30  1  0  0  0  0
 23 30  1  0  0  0  0
 30 31  1  0  0  0  0
 11 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
  8 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
  5 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
  3 39  1  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0313287

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(OC3=CC(O)=C(C4OC(CO)C(O)C(O)C4OC4OCC(O)(CO)C4O)C(O)=C3C2=O)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O15/c1-36-12-2-8-11(3-9(12)28)38-13-4-10(29)15(19(32)16(13)17(8)30)21-22(20(33)18(31)14(5-26)39-21)40-24-23(34)25(35,6-27)7-37-24/h2-4,14,18,20-24,26-29,31-35H,5-7H2,1H3

> <INCHI_KEY>
GTRLQDJSEMBQNI-UHFFFAOYSA-N

> <FORMULA>
C25H28O15

> <MOLECULAR_WEIGHT>
568.484

> <EXACT_MASS>
568.142820202

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.90788865842519

> <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)-1,3,6-trihydroxy-7-methoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-1.492546975333334

> <ALOGPS_LOGS>
-1.98

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.912002836846231

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.047221330969865

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423791325182915

> <JCHEM_POLAR_SURFACE_AREA>
245.28999999999996

> <JCHEM_REFRACTIVITY>
129.0107

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.02e+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)-1,3,6-trihydroxy-7-methoxyxanthen-9-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      14.670  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      16.004  -0.000   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      14.670  -2.310   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      16.004  -3.080   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.337  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      16.077  -4.764   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      17.108  -5.908   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      16.338  -7.242   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      17.745  -7.868   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      15.862  -8.706   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      16.892  -9.851   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      14.831  -6.922   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      13.687  -7.952   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   39                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   37                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   35                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   32                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28   30                                             
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28                                                            
CONECT   30   26   23   31                                                  
CONECT   31   30                                                            
CONECT   32   11   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34    8   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36    5   38                                                  
CONECT   38   37   39                                                       
CONECT   39   38    3   40                                                  
CONECT   40   39                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₅

Average Mass

568.4840 Da

Monoisotopic Mass

568.14282 Da

IUPAC Name

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

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(OC3=CC(O)=C(C4OC(CO)C(O)C(O)C4OC4OCC(O)(CO)C4O)C(O)=C3C2=O)C=C1O

InChI Identifier

InChI=1S/C25H28O15/c1-36-12-2-8-11(3-9(12)28)38-13-4-10(29)15(19(32)16(13)17(8)30)21-22(20(33)18(31)14(5-26)39-21)40-24-23(34)25(35,6-27)7-37-24/h2-4,14,18,20-24,26-29,31-35H,5-7H2,1H3

InChI Key

GTRLQDJSEMBQNI-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 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
Glycosyl compound
O-glycosyl compound
Anisole
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Benzenoid
Oxane
Tertiary alcohol
Vinylogous acid
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Polyol
Oxacycle
Ether
Acetal
Dialkyl ether
Alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Primary alcohol
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	-0.47	ALOGPS
logP	-1.5	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	7.05	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	245.29 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	129.01 m³·mol⁻¹	ChemAxon
Polarizability	54.91 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

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

137796510

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)-1,3,6-trihydroxy-7-methoxyxanthen-9-one (NP0313287)

MOL for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

3D MOL for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

3D SDF for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

3D-SDF for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

PDB for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

3D PDB for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

SMILES for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

INCHI for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

Structure for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)

3D Structure for NP0313287 (2-(3-{[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)-1,3,6-trihydroxy-7-methoxyxanthen-9-one)