NP-MRD: Showing NP-Card for 3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one (NP0185371)

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Record Information

Version

2.0

Created at

2022-09-04 00:45:20 UTC

Updated at

2022-09-04 00:45:20 UTC

NP-MRD ID

NP0185371

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one

Description

3-(4-{[6-({[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxy-4H-chromen-4-one belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. 3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one is found in Dalbergia sissoo and Glycosmis pentaphylla. 3-(4-{[6-({[3,4-Dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxy-4H-chromen-4-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251506592D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251506592D          

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    8.5737   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 C   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
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  2  0  0  0  0
  3 14  1  0  0  0  0
 10 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 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
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 28 32  1  0  0  0  0
 25 32  1  0  0  0  0
 32 33  1  0  0  0  0
 22 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  1  0  0  0  0
 20 38  1  0  0  0  0
 38 39  1  0  0  0  0
 18 40  1  0  0  0  0
 40 41  2  0  0  0  0
 15 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0185371

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O)=C2C(=O)C(=COC2=C1)C1=CC=C(OC2OC(COC3OCC(O)(CO)C3O)C(O)C(O)C2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O14/c1-36-14-6-16(29)19-17(7-14)37-8-15(20(19)30)12-2-4-13(5-3-12)40-25-23(33)22(32)21(31)18(41-25)9-38-26-24(34)27(35,10-28)11-39-26/h2-8,18,21-26,28-29,31-35H,9-11H2,1H3

> <INCHI_KEY>
SKCGEXKDKBCXKB-UHFFFAOYSA-N

> <FORMULA>
C27H30O14

> <MOLECULAR_WEIGHT>
578.523

> <EXACT_MASS>
578.163555646

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
56.70050689290707

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxy-4H-chromen-4-one

> <ALOGPS_LOGP>
0.22

> <JCHEM_LOGP>
-0.3218007076666664

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.701754799045773

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.333538256699263

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1423790163389214

> <JCHEM_POLAR_SURFACE_AREA>
214.05999999999997

> <JCHEM_REFRACTIVITY>
134.9798

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.22e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-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  -4.620   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       6.668  -0.770   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  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669   1.540   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      16.004   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      18.672   1.540   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      20.005   2.310   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      20.166   3.842   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      21.673   4.162   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      22.443   2.828   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      23.688   3.733   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      23.473   1.684   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      24.979   2.004   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      21.412   1.684   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      21.732   0.177   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      16.004  -0.000   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      17.338  -0.770   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      14.670  -0.770   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      14.670  -2.310   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      12.003  -0.770   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   13                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    7   14                                                  
CONECT   14   13    3                                                       
CONECT   15   10   16   41                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   40                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   38                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   30   32                                             
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30                                                            
CONECT   32   28   25   33                                                  
CONECT   33   32                                                            
CONECT   34   22   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   20   39                                                  
CONECT   39   38                                                            
CONECT   40   18   41                                                       
CONECT   41   40   15                                                       
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₁₄

Average Mass

578.5230 Da

Monoisotopic Mass

578.16356 Da

IUPAC Name

3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxy-4H-chromen-4-one

Traditional Name

3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC(O)=C2C(=O)C(=COC2=C1)C1=CC=C(OC2OC(COC3OCC(O)(CO)C3O)C(O)C(O)C2O)C=C1

InChI Identifier

InChI=1S/C27H30O14/c1-36-14-6-16(29)19-17(7-14)37-8-15(20(19)30)12-2-4-13(5-3-12)40-25-23(33)22(32)21(31)18(41-25)9-38-26-24(34)27(35,10-28)11-39-26/h2-8,18,21-26,28-29,31-35H,9-11H2,1H3

InChI Key

SKCGEXKDKBCXKB-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
Dalbergia sissoo	LOTUS Database	35616633
Glycosmis pentaphylla	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Germacranolides and derivatives

Alternative Parents

Substituents

Germacranolide
Germacrane sesquiterpenoid
Sesquiterpenoid
Gamma butyrolactone
Tetrahydrofuran
Carboxylic acid ester
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Carbonyl group
Alcohol
Organooxygen compound
Primary alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	0.22	ALOGPS
logP	-0.32	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	7.33	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	214.06 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	134.98 m³·mol⁻¹	ChemAxon
Polarizability	56.7 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

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 3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one (NP0185371)

MOL for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

3D MOL for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

3D SDF for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

3D-SDF for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

PDB for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

3D PDB for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

SMILES for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

INCHI for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

Structure for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)

3D Structure for NP0185371 (3-(4-{[6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}phenyl)-5-hydroxy-7-methoxychromen-4-one)