NP-MRD: Showing NP-Card for 3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid (NP0190787)

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Record Information

Version

2.0

Created at

2022-09-04 07:31:39 UTC

Updated at

2022-09-04 07:31:39 UTC

NP-MRD ID

NP0190787

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid

Description

Calycosin-7-O-beta-D-glucoside-6''-O-malonate belongs to the class of organic compounds known as isoflavonoid o-glycosides. These are o-glycosylated derivatives of isoflavonoids, which are natural products derived from 3-phenylchromen-4-one. 3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid is found in Astragalus membranaceus, Astragalus mongholicus and Trifolium pratense. Based on a literature review very few articles have been published on Calycosin-7-O-beta-D-glucoside-6''-O-malonate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042209312D          

 38 41  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309042209312D          

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 36 37  2  0  0  0  0
  3 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0190787

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C=C1O)C1=COC2=CC(O[C@@H]3O[C@H](COC(=O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]3O)=CC=C2C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H24O13/c1-34-16-5-2-11(6-15(16)26)14-9-35-17-7-12(3-4-13(17)21(14)30)37-25-24(33)23(32)22(31)18(38-25)10-36-20(29)8-19(27)28/h2-7,9,18,22-26,31-33H,8,10H2,1H3,(H,27,28)/t18-,22-,23+,24-,25-/m1/s1

> <INCHI_KEY>
KNBDAYPNFRHTOM-GOZZSVHWSA-N

> <FORMULA>
C25H24O13

> <MOLECULAR_WEIGHT>
532.454

> <EXACT_MASS>
532.121690833

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
51.29451730431848

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxo-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxo-4H-chromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid

> <JCHEM_LOGP>
0.6380522086666672

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.206880397297585

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3795979349337055

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649103025377329

> <JCHEM_POLAR_SURFACE_AREA>
198.51

> <JCHEM_REFRACTIVITY>
123.8052

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-oxo-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  C   UNK     0     -18.672  18.480   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0     -17.338  19.250   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0     -16.004  18.480   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0     -14.670  19.250   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0     -13.337  18.480   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -13.337  16.940   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0     -12.003  16.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0     -10.669  16.940   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -9.336  16.170   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -9.336  14.630   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -8.002  13.860   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -8.002  12.320   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -6.668  11.550   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -6.668  10.010   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.335   9.240   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -5.335   7.700   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.667   7.700   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.334   6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.334   5.390   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       0.000   7.700   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667   7.700   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.334   5.390   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -6.668   6.930   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -6.668   5.390   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -8.002   7.700   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -9.336   6.930   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -8.002   9.240   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -9.336  10.010   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -9.336  11.550   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0     -10.669  12.320   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0     -10.669  13.860   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0     -12.003  14.630   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0     -13.337  13.860   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0     -14.670  16.170   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -16.004  16.940   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -17.338  16.170   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   36                                                  
CONECT    7    6    8   34                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   33                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   31                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   29                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   16   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   14   30                                                  
CONECT   30   29                                                            
CONECT   31   12   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   10   34                                                  
CONECT   34   33    7   35                                                  
CONECT   35   34                                                            
CONECT   36    6   37                                                       
CONECT   37   36    3   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
Calycosin-7-O-b-D-glucoside-6''-O-malonate	Generator
Calycosin-7-O-b-D-glucoside-6''-O-malonic acid	Generator
Calycosin-7-O-beta-D-glucoside-6''-O-malonic acid	Generator
Calycosin-7-O-β-D-glucoside-6''-O-malonate	Generator
Calycosin-7-O-β-D-glucoside-6''-O-malonic acid	Generator

Chemical Formula

C₂₅H₂₄O₁₃

Average Mass

532.4540 Da

Monoisotopic Mass

532.12169 Da

IUPAC Name

3-oxo-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxo-4H-chromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid

Traditional Name

3-oxo-3-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C=C1O)C1=COC2=CC(O[C@@H]3O[C@H](COC(=O)CC(O)=O)[C@@H](O)[C@H](O)[C@H]3O)=CC=C2C1=O

InChI Identifier

InChI=1S/C25H24O13/c1-34-16-5-2-11(6-15(16)26)14-9-35-17-7-12(3-4-13(17)21(14)30)37-25-24(33)23(32)22(31)18(38-25)10-36-20(29)8-19(27)28/h2-7,9,18,22-26,31-33H,8,10H2,1H3,(H,27,28)/t18-,22-,23+,24-,25-/m1/s1

InChI Key

KNBDAYPNFRHTOM-GOZZSVHWSA-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
Astragalus membranaceus	LOTUS Database	35616633
Astragalus mongholicus	LOTUS Database	35616633
Trifolium pratense	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoflavonoid o-glycosides. These are o-glycosylated derivatives of isoflavonoids, which are natural products derived from 3-phenylchromen-4-one.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Isoflavonoid O-glycosides

Direct Parent

Isoflavonoid O-glycosides

Alternative Parents

Substituents

Isoflavonoid o-glycoside
Isoflavonoid-7-o-glycoside
4p-o-methylisoflavone
3'-hydroxy,4'-methoxyisoflavonoid
Isoflavone
Hydroxyisoflavonoid
Phenolic glycoside
Glycosyl compound
O-glycosyl compound
Chromone
Methoxyphenol
1-benzopyran
Benzopyran
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
Pyranone
Phenol
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Pyran
Oxane
Monocyclic benzene moiety
Monosaccharide
Dicarboxylic acid or derivatives
1,3-dicarbonyl compound
Benzenoid
Heteroaromatic compound
Carboxylic acid ester
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Polyol
Carboxylic acid
Ether
Alcohol
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organooxygen compound
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	0.64	ChemAxon
pKa (Strongest Acidic)	3.38	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	198.51 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	123.81 m³·mol⁻¹	ChemAxon
Polarizability	51.29 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

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

57378778

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid (NP0190787)

MOL for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

3D MOL for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

3D SDF for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

3D-SDF for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

PDB for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

3D PDB for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

SMILES for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

INCHI for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

Structure for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)

3D Structure for NP0190787 (3-oxo-3-{[(2r,3s,4s,5r,6s)-3,4,5-trihydroxy-6-{[3-(3-hydroxy-4-methoxyphenyl)-4-oxochromen-7-yl]oxy}oxan-2-yl]methoxy}propanoic acid)