NP-MRD: Showing NP-Card for 3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde (NP0218295)

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Record Information

Version

2.0

Created at

2022-09-05 18:54:52 UTC

Updated at

2022-09-05 18:54:52 UTC

NP-MRD ID

NP0218295

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde

Description

3-[(2H-1,3-benzodioxol-5-yl)methyl]-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-1-benzopyran-8-carbaldehyde belongs to the class of organic compounds known as homoisoflavanones. These are homoisoflavonoids with a structure based on the chromanone system. Chromanone is a bicyclic compound consisting of a 3,4-dihydro-1-benzopyran, which bears a ketone group at the 4-position. 3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde is found in Ophiopogon japonicus. 3-[(2H-1,3-benzodioxol-5-yl)methyl]-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-1-benzopyran-8-carbaldehyde is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004191515392D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004191515392D          

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 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  0  0  0  0
  6 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 19 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  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 30 34  1  0  0  0  0
 34 35  2  0  0  0  0
 27 35  1  0  0  0  0
 25 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
  3 38  1  0  0  0  0
 22 38  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0218295

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(C)C(OC2OC(CO)C(O)C(O)C2O)=C(C=O)C2=C1C(=O)C(CC1=CC=C3OCOC3=C1)CO2

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O12/c1-11-23(38-26-22(32)21(31)20(30)17(8-28)37-26)14(7-27)25-18(24(11)33-2)19(29)13(9-34-25)5-12-3-4-15-16(6-12)36-10-35-15/h3-4,6-7,13,17,20-22,26,28,30-32H,5,8-10H2,1-2H3

> <INCHI_KEY>
GSIZMWIFEPCTDO-UHFFFAOYSA-N

> <FORMULA>
C26H28O12

> <MOLECULAR_WEIGHT>
532.498

> <EXACT_MASS>
532.158076342

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
51.885704924714275

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(2H-1,3-benzodioxol-5-yl)methyl]-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-1-benzopyran-8-carbaldehyde

> <ALOGPS_LOGP>
0.53

> <JCHEM_LOGP>
0.5527752650000003

> <ALOGPS_LOGS>
-3.03

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.181571934907641

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.198423901682151

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092347475956

> <JCHEM_POLAR_SURFACE_AREA>
170.43999999999997

> <JCHEM_REFRACTIVITY>
128.31539999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.01e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(2H-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -4.001  -5.390   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  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.682  -9.206   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       6.150  -9.367   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.524  -7.960   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   38                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    8   18                                                  
CONECT   18   17                                                            
CONECT   19    6   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   23   38                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   36                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   35                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   34                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   30   35                                                  
CONECT   35   34   27                                                       
CONECT   36   25   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36    3   22                                                  
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₂₈O₁₂

Average Mass

532.4980 Da

Monoisotopic Mass

532.15808 Da

IUPAC Name

3-[(2H-1,3-benzodioxol-5-yl)methyl]-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-1-benzopyran-8-carbaldehyde

Traditional Name

3-(2H-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde

CAS Registry Number

Not Available

SMILES

COC1=C(C)C(OC2OC(CO)C(O)C(O)C2O)=C(C=O)C2=C1C(=O)C(CC1=CC=C3OCOC3=C1)CO2

InChI Identifier

InChI=1S/C26H28O12/c1-11-23(38-26-22(32)21(31)20(30)17(8-28)37-26)14(7-27)25-18(24(11)33-2)19(29)13(9-34-25)5-12-3-4-15-16(6-12)36-10-35-15/h3-4,6-7,13,17,20-22,26,28,30-32H,5,8-10H2,1-2H3

InChI Key

GSIZMWIFEPCTDO-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
Ophiopogon japonicus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as homoisoflavanones. These are homoisoflavonoids with a structure based on the chromanone system. Chromanone is a bicyclic compound consisting of a 3,4-dihydro-1-benzopyran, which bears a ketone group at the 4-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Homoisoflavonoids

Sub Class

Homoisoflavans

Direct Parent

Homoisoflavanones

Alternative Parents

Substituents

Homoisoflavanone
Phenolic glycoside
Hexose monosaccharide
Chromone
Glycosyl compound
O-glycosyl compound
Chromane
Benzopyran
1-benzopyran
Benzodioxole
Aryl alkyl ketone
Aryl ketone
Anisole
Aryl-aldehyde
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Ketone
Secondary alcohol
Oxacycle
Ether
Acetal
Polyol
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Primary alcohol
Aldehyde
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	0.53	ALOGPS
logP	0.55	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	170.44 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	128.32 m³·mol⁻¹	ChemAxon
Polarizability	51.89 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

75236483

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde (NP0218295)

MOL for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

3D MOL for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

3D SDF for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

3D-SDF for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

PDB for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

3D PDB for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

SMILES for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

INCHI for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

Structure for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)

3D Structure for NP0218295 (3-(2h-1,3-benzodioxol-5-ylmethyl)-5-methoxy-6-methyl-4-oxo-7-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2,3-dihydro-1-benzopyran-8-carbaldehyde)