NP-MRD: Showing NP-Card for 1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one (NP0280884)

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Record Information

Version

2.0

Created at

2022-09-09 06:55:18 UTC

Updated at

2022-09-09 06:55:19 UTC

NP-MRD ID

NP0280884

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one is found in Gentiana lutea.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305221920052D          

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  Mrv1652305221920052D          

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 33 23  1  0  0  0  0
 34  1  1  0  0  0  0
 34 10  1  0  0  0  0
 35  7  1  0  0  0  0
 35 24  1  0  0  0  0
 36  8  1  0  0  0  0
 36 24  1  0  0  0  0
 37  9  1  0  0  0  0
 37 25  1  0  0  0  0
 38 14  1  0  0  0  0
 38 15  1  0  0  0  0
 39 16  1  0  0  0  0
 39 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0280884

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O)=C2C(=O)C3=C(OC2=C1)C=CC(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)=C3

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O14/c1-34-10-5-12(26)17-15(6-10)38-14-3-2-9(4-11(14)18(17)28)37-25-23(33)21(31)20(30)16(39-25)8-36-24-22(32)19(29)13(27)7-35-24/h2-6,13,16,19-27,29-33H,7-8H2,1H3

> <INCHI_KEY>
KDXQJCRCDRBRFU-UHFFFAOYSA-N

> <FORMULA>
C25H28O14

> <MOLECULAR_WEIGHT>
552.4814

> <EXACT_MASS>
552.147905604

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
53.615756998249566

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.43

> <JCHEM_LOGP>
-0.5637304856666664

> <ALOGPS_LOGS>
-2.25

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.9226955314588

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.332246099226692

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526580404084756

> <JCHEM_POLAR_SURFACE_AREA>
214.05999999999995

> <JCHEM_REFRACTIVITY>
125.83649999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.08e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -0.000   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      20.005  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.004   1.540   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  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.339  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.670   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      21.339   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      20.005   2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      18.672   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      22.673  -0.770   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      22.673   2.310   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      16.004   4.620   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      13.337   6.160   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      20.005   3.850   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -0.000   4.620   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      18.672  -0.000   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      17.338   2.310   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      13.337   1.540   0.000  0.00  0.00           O+0
CONECT    1   34                                                            
CONECT    2    3    9                                                       
CONECT    3    2   14                                                       
CONECT    4    9   11                                                       
CONECT    5   10   12                                                       
CONECT    6   10   15                                                       
CONECT    7   13   35                                                       
CONECT    8   16   36                                                       
CONECT    9    2    4   37                                                  
CONECT   10    5    6   34                                                  
CONECT   11    4   14   18                                                  
CONECT   12    5   17   26                                                  
CONECT   13    7   19   27                                                  
CONECT   14    3   11   38                                                  
CONECT   15    6   17   38                                                  
CONECT   16    8   20   39                                                  
CONECT   17   12   15   18                                                  
CONECT   18   11   17   28                                                  
CONECT   19   13   22   29                                                  
CONECT   20   16   21   30                                                  
CONECT   21   20   23   31                                                  
CONECT   22   19   24   32                                                  
CONECT   23   21   25   33                                                  
CONECT   24   22   35   36                                                  
CONECT   25   23   37   39                                                  
CONECT   26   12                                                            
CONECT   27   13                                                            
CONECT   28   18                                                            
CONECT   29   19                                                            
CONECT   30   20                                                            
CONECT   31   21                                                            
CONECT   32   22                                                            
CONECT   33   23                                                            
CONECT   34    1   10                                                       
CONECT   35    7   24                                                       
CONECT   36    8   24                                                       
CONECT   37    9   25                                                       
CONECT   38   14   15                                                       
CONECT   39   16   25                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₄

Average Mass

552.4814 Da

Monoisotopic Mass

552.14791 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)C3=C(OC2=C1)C=CC(OC1OC(COC2OCC(O)C(O)C2O)C(O)C(O)C1O)=C3

InChI Identifier

InChI=1S/C25H28O14/c1-34-10-5-12(26)17-15(6-10)38-14-3-2-9(4-11(14)18(17)28)37-25-23(33)21(31)20(30)16(39-25)8-36-24-22(32)19(29)13(27)7-35-24/h2-6,13,16,19-27,29-33H,7-8H2,1H3

InChI Key

KDXQJCRCDRBRFU-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 lutea	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
Chromone
Disaccharide
Glycosyl compound
O-glycosyl compound
Anisole
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Oxane
Benzenoid
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Polyol
Ether
Acetal
Oxacycle
Alcohol
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
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	-0.43	ALOGPS
logP	-0.56	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	8.33	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	214.06 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	125.84 m³·mol⁻¹	ChemAxon
Polarizability	53.62 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

FDB002831

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-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one (NP0280884)

MOL for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

3D MOL for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

3D SDF for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

3D-SDF for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

PDB for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

3D PDB for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

SMILES for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

INCHI for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

Structure for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)

3D Structure for NP0280884 (1-hydroxy-3-methoxy-7-[(3,4,5-trihydroxy-6-{[(3,4,5-trihydroxyoxan-2-yl)oxy]methyl}oxan-2-yl)oxy]xanthen-9-one)