NP-MRD: Showing NP-Card for Epicatechin 6-C-glucoside (NP0048761)

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Record Information

Version

2.0

Created at

2022-03-17 21:01:46 UTC

Updated at

2022-03-17 21:01:46 UTC

NP-MRD ID

NP0048761

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Epicatechin 6-C-glucoside

Description

(-)-Epicatechin 6-C-glucoside, also known as 6-C-glucopyranosylepicatechin, belongs to the class of organic compounds known as flavonoid c-glycosides. Flavonoid C-glycosides are compounds containing a carbohydrate moiety which is C-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone (-)-Epicatechin 6-C-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (-)-Epicatechin 6-C-glucoside has been detected, but not quantified in, chinese cinnamons and herbs and spices. Epicatechin 6-C-glucoside is found in Rheum sp. and Rheum spp.. This could make (-)-epicatechin 6-C-glucoside a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241209352D          

 32 35  0  0  0  0            999 V2000
   -1.2964   -2.5928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -3.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5820   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5820   -3.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325   -2.5928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8470   -3.8304    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8470   -3.0053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5614   -2.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759   -1.3553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5614   -1.7678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759   -3.0054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9904   -2.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9904   -1.7678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7048   -1.3553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7048   -3.0053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5614   -4.2429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7254   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7254   -2.5929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -5.0679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4398   -3.8304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -4.2429    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1543   -5.0679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4398   -5.4804    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7254   -5.0679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8688   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5832   -4.2429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8688   -5.4804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4398   -6.3054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -5.4804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  6  2  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  6  0  0  0
 13 11  1  0  0  0  0
 11 14  2  0  0  0  0
 12 13  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 19  1  6  0  0  0
  2 21  1  0  0  0  0
  4 22  1  0  0  0  0
 27 20  1  0  0  0  0
 23 20  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
 24 28  1  1  0  0  0
 28 29  1  0  0  0  0
 25 30  1  6  0  0  0
 26 31  1  1  0  0  0
 27 32  1  6  0  0  0
 20  3  1  0  0  0  0
M  END


  Mrv0541 02241209352D          

 32 35  0  0  0  0            999 V2000
   -1.2964   -2.5928    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -3.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5820   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5820   -3.0053    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325   -2.5928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1325   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8470   -3.8304    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8470   -3.0053    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5614   -2.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759   -1.3553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5614   -1.7678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2759   -3.0054    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9904   -2.5929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9904   -1.7678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7048   -1.3553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7048   -3.0053    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5614   -4.2429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7254   -4.2429    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7254   -2.5929    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2964   -5.0679    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4398   -3.8304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1543   -4.2429    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.1543   -5.0679    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4398   -5.4804    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7254   -5.0679    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.8688   -3.8304    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5832   -4.2429    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8688   -5.4804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4398   -6.3054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0109   -5.4804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  1  6  2  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  7 10  1  0  0  0  0
 10 11  1  6  0  0  0
 13 11  1  0  0  0  0
 11 14  2  0  0  0  0
 12 13  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
  9 19  1  6  0  0  0
  2 21  1  0  0  0  0
  4 22  1  0  0  0  0
 27 20  1  0  0  0  0
 23 20  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
 24 28  1  1  0  0  0
 28 29  1  0  0  0  0
 25 30  1  6  0  0  0
 26 31  1  1  0  0  0
 27 32  1  6  0  0  0
 20  3  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048761

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1OC([C@H](O)[C@@H](O)[C@@H]1O)C1=C(O)C=C2O[C@@H]([C@H](O)CC2=C1O)C1=CC(O)=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C21H24O11/c22-6-14-17(28)18(29)19(30)21(32-14)15-11(25)5-13-8(16(15)27)4-12(26)20(31-13)7-1-2-9(23)10(24)3-7/h1-3,5,12,14,17-30H,4,6H2/t12-,14-,17-,18+,19-,20-,21?/m1/s1

> <INCHI_KEY>
PWMSPKVTJLJDDS-NOCOPWLTSA-N

> <FORMULA>
C21H24O11

> <MOLECULAR_WEIGHT>
452.4087

> <EXACT_MASS>
452.13186161

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
44.847449352552374

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2-(3,4-dihydroxyphenyl)-6-[(3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <ALOGPS_LOGP>
-0.64

> <JCHEM_LOGP>
-0.9622138896666665

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.38099296581375

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.781192058058062

> <JCHEM_PKA_STRONGEST_BASIC>
-3.292320040483612

> <JCHEM_POLAR_SURFACE_AREA>
200.52999999999997

> <JCHEM_REFRACTIVITY>
107.11799999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.77e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-C-glucopyranosylepicatechin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.420  -4.840   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.754  -5.610   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.754  -7.150   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.420  -7.920   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.086  -7.150   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.086  -5.610   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.247  -4.840   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.247  -7.920   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.581  -7.150   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.581  -5.610   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.915  -4.840   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.248  -2.530   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.915  -3.300   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.248  -5.610   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.582  -4.840   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.582  -3.300   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.916  -2.530   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       6.916  -5.610   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.915  -7.920   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -5.087  -7.920   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -5.087  -4.840   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -2.420  -9.460   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -6.421  -7.150   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -7.755  -7.920   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -7.755  -9.460   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -6.421 -10.230   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -5.087  -9.460   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -9.088  -7.150   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0     -10.422  -7.920   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -9.088 -10.230   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -6.421 -11.770   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -3.754 -10.230   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   21                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5   22                                                  
CONECT    5    4    6    8                                                  
CONECT    6    1    7    5                                                  
CONECT    7    6   10                                                       
CONECT    8    5    9                                                       
CONECT    9    8   10   19                                                  
CONECT   10    9    7   11                                                  
CONECT   11   10   13   14                                                  
CONECT   12   13   16                                                       
CONECT   13   11   12                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   12   17                                                  
CONECT   17   16                                                            
CONECT   18   15                                                            
CONECT   19    9                                                            
CONECT   20   27   23    3                                                  
CONECT   21    2                                                            
CONECT   22    4                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24   26   30                                                  
CONECT   26   25   27   31                                                  
CONECT   27   20   26   32                                                  
CONECT   28   24   29                                                       
CONECT   29   28                                                            
CONECT   30   25                                                            
CONECT   31   26                                                            
CONECT   32   27                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Value	Source
6-C-Glucopyranosylepicatechin	HMDB
6-Glucopyranosyl-(-)-epicatechin	HMDB
6-Glucosyl-(-)-epicatechin	HMDB

Chemical Formula

C₂₁H₂₄O₁₁

Average Mass

452.4087 Da

Monoisotopic Mass

452.13186 Da

IUPAC Name

(2R,3R)-2-(3,4-dihydroxyphenyl)-6-[(3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

6-C-glucopyranosylepicatechin

CAS Registry Number

103215-49-2

SMILES

OC[C@H]1OC([C@H](O)[C@@H](O)[C@@H]1O)C1=C(O)C=C2O[C@@H]([C@H](O)CC2=C1O)C1=CC(O)=C(O)C=C1

InChI Identifier

InChI=1S/C21H24O11/c22-6-14-17(28)18(29)19(30)21(32-14)15-11(25)5-13-8(16(15)27)4-12(26)20(31-13)7-1-2-9(23)10(24)3-7/h1-3,5,12,14,17-30H,4,6H2/t12-,14-,17-,18+,19-,20-,21?/m1/s1

InChI Key

PWMSPKVTJLJDDS-NOCOPWLTSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cinnamomum aromaticum	FooDB	KNAPSACK
Rheum sp.	Plant	KNApSAcK
Rheum spp.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid c-glycosides. Flavonoid C-glycosides are compounds containing a carbohydrate moiety which is C-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 C-glycosides

Alternative Parents

Substituents

Catechin
Flavonoid c-glycoside
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavan-3-ol
Hydroxyflavonoid
Flavan
Phenolic glycoside
Hexose monosaccharide
C-glycosyl compound
Glycosyl compound
Chromane
Benzopyran
1-benzopyran
Catechol
Phenol
Alkyl aryl ether
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Monosaccharide
Oxane
Monocyclic benzene moiety
Benzenoid
Secondary alcohol
Polyol
Oxacycle
Ether
Dialkyl ether
Organoheterocyclic compound
Alcohol
Organic oxygen compound
Primary alcohol
Hydrocarbon derivative
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	-0.64	ALOGPS
logP	-0.96	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	8.78	ChemAxon
pKa (Strongest Basic)	-3.3	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	107.12 m³·mol⁻¹	ChemAxon
Polarizability	44.85 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	No	ChemAxon

External Links

HMDB ID

HMDB0037399

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB016443

KNApSAcK ID

C00006356

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

131752183

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Epicatechin 6-C-glucoside (NP0048761)

MOL for NP0048761 (Epicatechin 6-C-glucoside)

3D MOL for NP0048761 (Epicatechin 6-C-glucoside)

3D SDF for NP0048761 (Epicatechin 6-C-glucoside)

3D-SDF for NP0048761 (Epicatechin 6-C-glucoside)

PDB for NP0048761 (Epicatechin 6-C-glucoside)

3D PDB for NP0048761 (Epicatechin 6-C-glucoside)

SMILES for NP0048761 (Epicatechin 6-C-glucoside)

INCHI for NP0048761 (Epicatechin 6-C-glucoside)

Structure for NP0048761 (Epicatechin 6-C-glucoside)

3D Structure for NP0048761 (Epicatechin 6-C-glucoside)