NP-MRD: Showing NP-Card for (2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0330976)

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Record Information

Version

1.0

Created at

2022-09-12 16:50:59 UTC

Updated at

2022-09-12 16:50:59 UTC

NP-MRD ID

NP0330976

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol

Description

(2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol is found in Cassia fistula, Cassia javanica, Rumex acetosa and Ziziphus jujuba. Based on a literature review very few articles have been published on Epiafzelechin-(4beta-8)-epicatechin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122218512D          

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M  END

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  Mrv1652309122218512D          

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  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
  8 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 17 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  6  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
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  2  0  0  0  0
 27 34  1  0  0  0  0
 26 35  1  0  0  0  0
 35 36  1  6  0  0  0
 35 37  1  0  0  0  0
 23 37  1  0  0  0  0
 16 38  1  0  0  0  0
  6 38  1  0  0  0  0
 38 39  1  6  0  0  0
  5 40  1  0  0  0  0
 40 41  2  0  0  0  0
  2 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330976

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CC2=C(O[C@@H]1C1=CC=C(O)C(O)=C1)C([C@@H]1[C@@H](O)[C@H](OC3=CC(O)=CC(O)=C13)C1=CC=C(O)C=C1)=C(O)C=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C30H26O11/c31-14-4-1-12(2-5-14)29-27(39)26(24-20(36)8-15(32)9-23(24)40-29)25-21(37)11-18(34)16-10-22(38)28(41-30(16)25)13-3-6-17(33)19(35)7-13/h1-9,11,22,26-29,31-39H,10H2/t22-,26-,27-,28-,29-/m1/s1

> <INCHI_KEY>
KUODBSWFMJMVJV-NFJBMHMQSA-N

> <FORMULA>
C30H26O11

> <MOLECULAR_WEIGHT>
562.527

> <EXACT_MASS>
562.147511657

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
54.35734377909808

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-4-[(2R,3R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <JCHEM_LOGP>
3.419310335333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.193602284175489

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.758127682890152

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4601834882350033

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
144.5271

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4R)-4-[(2R,3R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.865  -0.931   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   41                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   40                                                  
CONECT    6    5    7   38                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   15                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    8   16                                                  
CONECT   16   15   17   38                                                  
CONECT   17   16   18   24                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   37                                                  
CONECT   24   23   17   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   35                                                  
CONECT   27   26   28   34                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   27                                                       
CONECT   35   26   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   23                                                       
CONECT   38   16    6   39                                                  
CONECT   39   38                                                            
CONECT   40    5   41                                                       
CONECT   41   40    2                                                       
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Value	Source
Epiafzelechin-(4b-8)-epicatechin	Generator
Epiafzelechin-(4β-8)-epicatechin	Generator

Chemical Formula

C₃₀H₂₆O₁₁

Average Mass

562.5270 Da

Monoisotopic Mass

562.14751 Da

IUPAC Name

(2R,3R,4R)-4-[(2R,3R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

(2R,3R,4R)-4-[(2R,3R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

CAS Registry Number

Not Available

SMILES

O[C@@H]1CC2=C(O[C@@H]1C1=CC=C(O)C(O)=C1)C([C@@H]1[C@@H](O)[C@H](OC3=CC(O)=CC(O)=C13)C1=CC=C(O)C=C1)=C(O)C=C2O

InChI Identifier

InChI=1S/C30H26O11/c31-14-4-1-12(2-5-14)29-27(39)26(24-20(36)8-15(32)9-23(24)40-29)25-21(37)11-18(34)16-10-22(38)28(41-30(16)25)13-3-6-17(33)19(35)7-13/h1-9,11,22,26-29,31-39H,10H2/t22-,26-,27-,28-,29-/m1/s1

InChI Key

KUODBSWFMJMVJV-NFJBMHMQSA-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
Cassia fistula	LOTUS Database	35616633
Cassia javanica	LOTUS Database	35616633
Rumex acetosa	LOTUS Database	35616633
Ziziphus jujuba	LOTUS Database	35616633

Chemical Taxonomy

Classification

Not classified

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	3.42	ChemAxon
pKa (Strongest Acidic)	8.76	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	200.53 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	144.53 m³·mol⁻¹	ChemAxon
Polarizability	54.36 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

8415324

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10239837

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0330976)

MOL for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D MOL for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D SDF for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D-SDF for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

PDB for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D PDB for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

SMILES for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

INCHI for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

Structure for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D Structure for NP0330976 ((2r,3r,4r)-4-[(2r,3r)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2h-1-benzopyran-8-yl]-2-(4-hydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)