NP-MRD: Showing NP-Card for 5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one (NP0060065)

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Record Information

Version

2.0

Created at

2022-04-28 05:11:01 UTC

Updated at

2022-04-28 05:11:01 UTC

NP-MRD ID

NP0060065

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one

Description

Lethedoside c belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. Thus, lethedoside c is considered to be a flavonoid. 5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one is found in Lethedon tannaensis . Based on a literature review very few articles have been published on Lethedoside c.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282207112D          

 36 39  0  0  1  0            999 V2000
   -1.4289   -2.4750    0.0000 C   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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -1.6500    0.0000 C   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
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1434   -1.2375    0.0000 C   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
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    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  2  0  0  0  0
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  8  9  1  0  0  0  0
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M  END

     RDKit          3D

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   -4.0672   -2.1471   -0.7216 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.2792   -0.5101   -0.7145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3494   -1.2354   -1.4884 O   0  0  0  0  0  0  0  0  0  0  0  0
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    4.4881    1.0650    1.1586 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8636    1.1016    1.2949 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.0121    0.3148    0.6542 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.4283    1.4385    1.0348 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.4451    1.9802   -0.3989 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1803   -0.8016   -0.9745 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652304282207112D          

 36 39  0  0  1  0            999 V2000
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    2.8579    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    3.5724    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0060065

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C2C(=O)C=C(OC2=C1)C1=CC(O)=C(OC)C(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H26O12/c1-31-11-6-15-19(16(7-11)35-24-22(30)21(29)20(28)18(9-25)36-24)12(26)8-14(34-15)10-4-13(27)23(33-3)17(5-10)32-2/h4-8,18,20-22,24-25,27-30H,9H2,1-3H3/t18-,20-,21+,22-,24-/m1/s1

> <INCHI_KEY>
WGZGLIQYUYIVRX-BKSKZGTRSA-N

> <FORMULA>
C24H26O12

> <MOLECULAR_WEIGHT>
506.46

> <EXACT_MASS>
506.142426277

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
50.30285425633345

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one

> <ALOGPS_LOGP>
0.81

> <JCHEM_LOGP>
-0.3808274350000005

> <ALOGPS_LOGS>
-3.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.200827325837402

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.5846968282951

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092346309512

> <JCHEM_POLAR_SURFACE_AREA>
173.6

> <JCHEM_REFRACTIVITY>
122.46699999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -6.668  -5.390   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -6.668  -6.930   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      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001  -2.310   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       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.002   4.620   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8                                                            
CONECT   10    4   11                                                       
CONECT   11   10                                                            
CONECT   12    2   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16   19                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   12                                                       
CONECT   19   15   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21   14                                                       
CONECT   23   21   24                                                       
CONECT   24   23                                                            
CONECT   25   19   26                                                       
CONECT   26   25   27   31                                                  
CONECT   27   26   28   36                                                  
CONECT   28   27   29   35                                                  
CONECT   29   28   30   34                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30   26                                                       
CONECT   32   30   33                                                       
CONECT   33   32                                                            
CONECT   34   29                                                            
CONECT   35   28                                                            
CONECT   36   27                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₂₆O₁₂

Average Mass

506.4600 Da

Monoisotopic Mass

506.14243 Da

IUPAC Name

2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4H-chromen-4-one

Traditional Name

2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}chromen-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=C2C(=O)C=C(OC2=C1)C1=CC(O)=C(OC)C(OC)=C1

InChI Identifier

InChI=1S/C24H26O12/c1-31-11-6-15-19(16(7-11)35-24-22(30)21(29)20(28)18(9-25)36-24)12(26)8-14(34-15)10-4-13(27)23(33-3)17(5-10)32-2/h4-8,18,20-22,24-25,27-30H,9H2,1-3H3/t18-,20-,21+,22-,24-/m1/s1

InChI Key

WGZGLIQYUYIVRX-BKSKZGTRSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Lethedon tannaensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
Flavonoid-5-o-glycoside
3p-methoxyflavonoid-skeleton
4p-methoxyflavonoid-skeleton
7-methoxyflavonoid-skeleton
Monohydroxyflavonoid
Hydroxyflavonoid
3'-hydroxyflavonoid
Flavone
Phenolic glycoside
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Chromone
1-benzopyran
O-dimethoxybenzene
Methoxyphenol
Benzopyran
Dimethoxybenzene
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Pyranone
Alkyl aryl ether
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Monocyclic benzene moiety
Benzenoid
Pyran
Oxane
Monosaccharide
Vinylogous ester
Heteroaromatic compound
Secondary alcohol
Ether
Organoheterocyclic compound
Oxacycle
Polyol
Acetal
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Organooxygen 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	0.81	ALOGPS
logP	-0.38	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	9.58	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	173.6 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	122.47 m³·mol⁻¹	ChemAxon
Polarizability	50.3 Å³	ChemAxon
Number of Rings	4	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

C00013719

Chemspider ID

8566913

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10391471

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one (NP0060065)

MOL for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

3D MOL for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

3D SDF for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

3D-SDF for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

PDB for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

3D PDB for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

SMILES for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

INCHI for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

Structure for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)

3D Structure for NP0060065 (5-(beta-D-Glucopyranosyloxy)-2-(3-hydroxy-4,5-dimethoxyphenyl)-7-methoxy-4H-1-benzopyran-4-one)