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Showing NP-Card for Epicatechin 3-glucoside (NP0048947)

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Record Information
Version2.0
Created at2022-03-17 21:04:42 UTC
Updated at2022-03-17 21:04:42 UTC
NP-MRD IDNP0048947
Secondary Accession NumbersNone
Natural Product Identification
Common NameEpicatechin 3-glucoside
DescriptionEpicatechin 3-glucoside belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position. Epicatechin 3-glucoside is found in Davallia mariesii, Excoecaria agallocha, Eysenhardtia subcoriacea Pennell, Mangifera indica, Pinus sylvestris and Quercus miyagii. Epicatechin 3-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0048947 (Epicatechin 3-glucoside)

Catechin 3-O-glucose
  Mrv1572001071617272D          

 32 35  0  0  0  0            999 V2000
    1.2503   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9648   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9648    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7510   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4655    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7510   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
  3 31  1  0  0  0  0
 31 32  1  0  0  0  0
M  END
Download

3D MOL for NP0048947 (Epicatechin 3-glucoside)

Download
3D SDF for NP0048947 (Epicatechin 3-glucoside)
Catechin 3-O-glucose
  Mrv1572001071617272D          

 32 35  0  0  0  0            999 V2000
    1.2503   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3221   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9648   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2503    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9648    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5358    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7510   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4655    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7510   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0365   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8931   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6076   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1787   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 13 20  1  0  0  0  0
 10 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 24 25  2  0  0  0  0
  9 25  1  0  0  0  0
 25 26  1  0  0  0  0
  5 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
  3 31  1  0  0  0  0
 31 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048947

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2CC3=C(OC2C2=CC(O)=C(O)C=C2)C=C(O)C=C3O)C(O)C(O)C1O

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

> <INCHI_KEY>
YOVYWMDLYSJYPO-UHFFFAOYSA-N

> <FORMULA>
C21H24O11

> <MOLECULAR_WEIGHT>
452.412

> <EXACT_MASS>
452.131861593

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
43.54106532891929

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.02

> <JCHEM_LOGP>
0.02427136966666618

> <ALOGPS_LOGS>
-2.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.622056653643083

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.00365037222607

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083556126551

> <JCHEM_POLAR_SURFACE_AREA>
189.52999999999997

> <JCHEM_REFRACTIVITY>
106.41299999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0048947 (Epicatechin 3-glucoside)
Download
PDB for NP0048947 (Epicatechin 3-glucoside)
HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Catechin 3-O-glucose                              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  O   UNK     0       2.334  -9.240   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.334  -7.700   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.000  -6.930   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.000  -5.390   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.334  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.334  -3.080   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.667  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.001  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.335  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.335  -0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.001   0.000   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.667  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.334   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.000  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.334   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.668  -0.770   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.334   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.668   2.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.000   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.334   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.668   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -7.002  -0.770   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -8.336   0.000   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -7.002  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.668  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -5.668  -4.620   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.667  -5.390   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.001  -4.620   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -1.667  -6.930   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.001  -7.700   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -0.334  -7.700   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -0.334  -9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   31                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   25                                                  
CONECT   10    9   11   21                                                  
CONECT   11   10   12                                                       
CONECT   12   11    7   13                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   13                                                       
CONECT   21   10   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24    9   26                                                  
CONECT   26   25                                                            
CONECT   27    5   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29    3   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

Download
3D PDB for NP0048947 (Epicatechin 3-glucoside)
Download
SMILES for NP0048947 (Epicatechin 3-glucoside)
OCC1OC(OC2CC3=C(OC2C2=CC(O)=C(O)C=C2)C=C(O)C=C3O)C(O)C(O)C1O
Download
INCHI for NP0048947 (Epicatechin 3-glucoside)
InChI=1S/C21H24O11/c22-7-16-17(27)18(28)19(29)21(32-16)31-15-6-10-12(25)4-9(23)5-14(10)30-20(15)8-1-2-11(24)13(26)3-8/h1-5,15-29H,6-7H2
Download
View in JSmol
Synonyms
ValueSource
Epicatechin 3-O-beta-D-glucopyranosideHMDB
Chemical FormulaC21H24O11
Average Mass452.4120 Da
Monoisotopic Mass452.13186 Da
IUPAC Name2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-3-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number103303-00-0
SMILES
OCC1OC(OC2CC3=C(OC2C2=CC(O)=C(O)C=C2)C=C(O)C=C3O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C21H24O11/c22-7-16-17(27)18(28)19(29)21(32-16)31-15-6-10-12(25)4-9(23)5-14(10)30-20(15)8-1-2-11(24)13(26)3-8/h1-5,15-29H,6-7H2
InChI KeyYOVYWMDLYSJYPO-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Cinnamomum aromaticumFooDB
Davallia mariesiiLOTUS Database
Excoecaria agallochaLOTUS Database
Eysenhardtia subcoriacea PennellPlant
Lens culinarisFooDB
Mangifera indicaLOTUS Database
Pinus sylvestrisLOTUS Database
Quercus miyagiiLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as flavonoid-3-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C3-position.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentFlavonoid-3-O-glycosides  
Alternative Parents
Substituents
  • Flavonoid-3-o-glycoside
    • 

  • Catechin
    • 

  • 3'-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 5-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • Flavan-3-ol
    • 

  • Hydroxyflavonoid
    • 

  • Flavan
    • 

  • Hexose monosaccharide
    • 

  • Glycosyl compound
    • 

  • O-glycosyl compound
    • 

  • Chromane
    • 

  • Benzopyran
    • 

  • 1-benzopyran
    • 

  • Catechol
    • 

  • Phenol
    • 

  • Alkyl aryl ether
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Oxane
    • 

  • Monosaccharide
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Secondary alcohol
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Ether
    • 

  • Organoheterocyclic compound
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.02ALOGPS
logP0.024ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)9ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area189.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity106.41 m³·mol⁻¹ChemAxon
Polarizability43.54 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0037943  
DrugBank IDNot Available
Phenol Explorer Compound ID199  
FoodDB IDFDB017113  
KNApSAcK IDC00008842  
Chemspider ID11209019  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14104301  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available