NP-MRD: Showing NP-Card for 5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one (NP0177445)

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Record Information

Version

2.0

Created at

2022-09-03 15:17:07 UTC

Updated at

2022-09-03 15:17:07 UTC

NP-MRD ID

NP0177445

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one

Description

CHEMBL88957 belongs to the class of organic compounds known as flavonolignans. These are non-conventional lignans that derived from flavonoids. They are characterized by a p-dioxin ring substituted at one carbon atom by a C3C6 (phenylpropan) group and fused to the B-ring of the 2-phenylchromene moiety. 5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one is found in Epimedium sagittatum. Based on a literature review very few articles have been published on CHEMBL88957.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032217172D          

 36 40  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.7171   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.8592   -3.7125    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 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032217172D          

 36 40  0  0  1  0            999 V2000
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0013   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0177445

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC=C(C=C2O[C@@H]1CO)C1=CC(=O)C2=C(O)C=C(O)C=C2O1

> <INCHI_IDENTIFIER>
InChI=1S/C26H22O10/c1-32-21-6-13(7-22(33-2)25(21)31)26-23(11-27)35-19-5-12(3-4-17(19)36-26)18-10-16(30)24-15(29)8-14(28)9-20(24)34-18/h3-10,23,26-29,31H,11H2,1-2H3/t23-,26-/m1/s1

> <INCHI_KEY>
LWFJEGQUKUEIRY-ZEQKJWHPSA-N

> <FORMULA>
C26H22O10

> <MOLECULAR_WEIGHT>
494.452

> <EXACT_MASS>
494.121296908

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
50.20392938847167

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-2-[(2R,3R)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-4H-chromen-4-one

> <JCHEM_LOGP>
3.058384373

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.149463653516742

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.576922210219812

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9904151517356974

> <JCHEM_POLAR_SURFACE_AREA>
144.14000000000001

> <JCHEM_REFRACTIVITY>
127.04299999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-[(2R,3R)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.003  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.337  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.337  -4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.670  -5.390   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      16.004  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      17.338  -5.390   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      18.672  -4.620   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      17.338  -6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      18.672  -7.700   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      20.005  -6.930   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      18.672  -9.240   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      17.338 -10.010   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      17.338 -11.550   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      16.004  -9.240   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      16.004  -7.700   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      14.670  -6.930   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.003  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   31                                                  
CONECT    6    5    7   28                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   26                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   25                                                  
CONECT   12   11   13   24                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   23                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   16   24                                                  
CONECT   24   23   12                                                       
CONECT   25   11   26                                                       
CONECT   26   25    8   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27    6   29                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31    5   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   32    3   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₂O₁₀

Average Mass

494.4520 Da

Monoisotopic Mass

494.12130 Da

IUPAC Name

5,7-dihydroxy-2-[(2R,3R)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-2-[(2R,3R)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC=C(C=C2O[C@@H]1CO)C1=CC(=O)C2=C(O)C=C(O)C=C2O1

InChI Identifier

InChI=1S/C26H22O10/c1-32-21-6-13(7-22(33-2)25(21)31)26-23(11-27)35-19-5-12(3-4-17(19)36-26)18-10-16(30)24-15(29)8-14(28)9-20(24)34-18/h3-10,23,26-29,31H,11H2,1-2H3/t23-,26-/m1/s1

InChI Key

LWFJEGQUKUEIRY-ZEQKJWHPSA-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
Epimedium sagittatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonolignans. These are non-conventional lignans that derived from flavonoids. They are characterized by a p-dioxin ring substituted at one carbon atom by a C3C6 (phenylpropan) group and fused to the B-ring of the 2-phenylchromene moiety.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Flavonolignans

Sub Class

Not Available

Direct Parent

Flavonolignans

Alternative Parents

Substituents

Flavonolignan
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Hydroxyflavonoid
2-phenylbenzo-1,4-dioxane
Phenylbenzodioxane
Chromone
M-dimethoxybenzene
Dimethoxybenzene
1-benzopyran
Benzo-1,4-dioxane
Benzodioxane
Benzopyran
Methoxyphenol
Methoxybenzene
Anisole
Phenoxy compound
Phenol ether
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Phenol
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Pyran
Para-dioxin
Heteroaromatic compound
Vinylogous acid
Ether
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
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	3.06	ChemAxon
pKa (Strongest Acidic)	6.58	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	144.14 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	127.04 m³·mol⁻¹	ChemAxon
Polarizability	50.2 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

8966657

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10791345

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one (NP0177445)

MOL for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

3D MOL for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

3D SDF for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

3D-SDF for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

PDB for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

3D PDB for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

SMILES for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

INCHI for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

Structure for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)

3D Structure for NP0177445 (5,7-dihydroxy-2-[(2r,3r)-2-(4-hydroxy-3,5-dimethoxyphenyl)-3-(hydroxymethyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one)