NP-MRD: Showing NP-Card for 1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one (NP0243718)

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Record Information

Version

2.0

Created at

2022-09-07 04:19:46 UTC

Updated at

2022-09-07 04:19:46 UTC

NP-MRD ID

NP0243718

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

1,3,7-Trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-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. 1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one is found in Gentiana asclepiadea. 1,3,7-Trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-9H-xanthen-9-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171520592D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004171520592D          

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    0.7145   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 O   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
   -2.1434   -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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  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
  9 10  1  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  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 16 25  1  0  0  0  0
 25 26  1  0  0  0  0
 15 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  2  0  0  0  0
 11 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
  9 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
  7 34  1  0  0  0  0
 34 35  1  0  0  0  0
  5 36  1  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  1  0  0  0  0
  3 40  1  0  0  0  0
 40 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0243718

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC3=C(C=C2O)C(=O)C2=C(O)C(C4OC(CO)C(O)C(O)C4O)=C(O)C=C2O3)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O16/c26-4-12-17(31)20(34)22(36)24(39-12)14-8(29)2-11-15(19(14)33)16(30)6-1-7(28)10(3-9(6)38-11)40-25-23(37)21(35)18(32)13(5-27)41-25/h1-3,12-13,17-18,20-29,31-37H,4-5H2

> <INCHI_KEY>
JPVYUZPSQZVPAO-UHFFFAOYSA-N

> <FORMULA>
C25H28O16

> <MOLECULAR_WEIGHT>
584.483

> <EXACT_MASS>
584.137734822

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
55.81015831483626

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.22

> <JCHEM_LOGP>
-2.6300100646666666

> <ALOGPS_LOGS>
-1.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.646756441201413

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.111019779596426

> <JCHEM_PKA_STRONGEST_BASIC>
-3.648395365939157

> <JCHEM_POLAR_SURFACE_AREA>
276.52

> <JCHEM_REFRACTIVITY>
130.00260000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.10e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -6.930   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       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      13.337  -4.620   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      16.004  -4.620   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      14.670  -6.930   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      16.004  -7.700   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      13.337  -7.700   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.337  -9.240   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.003  -6.930   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   40                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   36                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   34                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   32                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   29                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   27                                                  
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   16   26                                                  
CONECT   26   25                                                            
CONECT   27   15   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   11   30                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30    9   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33    7   35                                                  
CONECT   35   34                                                            
CONECT   36    5   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38    3   41                                                  
CONECT   41   40                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₆

Average Mass

584.4830 Da

Monoisotopic Mass

584.13773 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC3=C(C=C2O)C(=O)C2=C(O)C(C4OC(CO)C(O)C(O)C4O)=C(O)C=C2O3)C(O)C(O)C1O

InChI Identifier

InChI=1S/C25H28O16/c26-4-12-17(31)20(34)22(36)24(39-12)14-8(29)2-11-15(19(14)33)16(30)6-1-7(28)10(3-9(6)38-11)40-25-23(37)21(35)18(32)13(5-27)41-25/h1-3,12-13,17-18,20-29,31-37H,4-5H2

InChI Key

JPVYUZPSQZVPAO-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
Gentiana asclepiadea	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
Glycosyl compound
O-glycosyl compound
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Benzenoid
Pyran
Oxane
Monosaccharide
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Oxacycle
Polyol
Acetal
Dialkyl ether
Ether
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
Alcohol
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	-1.2	ALOGPS
logP	-2.6	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	7.11	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	276.52 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	130 m³·mol⁻¹	ChemAxon
Polarizability	55.81 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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one (NP0243718)

MOL for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

3D MOL for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

3D SDF for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

3D-SDF for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

PDB for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

3D PDB for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

SMILES for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

INCHI for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

Structure for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)

3D Structure for NP0243718 (1,3,7-trihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}xanthen-9-one)