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Showing NP-Card for Catechin 5-glucoside (NP0048948)

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Record Information
Version2.0
Created at2022-03-17 21:04:42 UTC
Updated at2022-03-17 21:04:43 UTC
NP-MRD IDNP0048948
Secondary Accession NumbersNone
Natural Product Identification
Common NameCatechin 5-glucoside
DescriptionCatechin 5-glucoside belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone. Catechin 5-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Catechin 5-glucoside has been detected, but not quantified in, garden rhubarbs and green vegetables. Catechin 5-glucoside is found in Davallia griffithiana, Davallia mariesii, Hypericum erectum Thunb., Polygonum cuspidatum , Rheum sp. and Rheum spp.. This could make catechin 5-glucoside a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0048948 (Catechin 5-glucoside)


  Mrv0541 05061310072D          

 32 35  0  0  0  0            999 V2000
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  8  1  1  0  0  0  0
  8  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  2  1  0  0  0  0
 12  3  1  0  0  0  0
 12 11  2  0  0  0  0
 13  6  1  0  0  0  0
 14  4  1  0  0  0  0
 14 10  2  0  0  0  0
 15  5  2  0  0  0  0
 15 10  1  0  0  0  0
 16  7  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 18  1  0  0  0  0
 20  8  1  0  0  0  0
 20 13  1  0  0  0  0
 21 19  1  0  0  0  0
 22  7  1  0  0  0  0
 23  9  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29 19  1  0  0  0  0
 30 14  1  0  0  0  0
 30 20  1  0  0  0  0
 31 15  1  0  0  0  0
 31 21  1  0  0  0  0
 32 16  1  0  0  0  0
 32 21  1  0  0  0  0
M  END
Download

3D MOL for NP0048948 (Catechin 5-glucoside)

Download
3D SDF for NP0048948 (Catechin 5-glucoside)

  Mrv0541 05061310072D          

 32 35  0  0  0  0            999 V2000
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  8  1  1  0  0  0  0
  8  3  2  0  0  0  0
  9  4  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  2  1  0  0  0  0
 12  3  1  0  0  0  0
 12 11  2  0  0  0  0
 13  6  1  0  0  0  0
 14  4  1  0  0  0  0
 14 10  2  0  0  0  0
 15  5  2  0  0  0  0
 15 10  1  0  0  0  0
 16  7  1  0  0  0  0
 17 16  1  0  0  0  0
 18 17  1  0  0  0  0
 19 18  1  0  0  0  0
 20  8  1  0  0  0  0
 20 13  1  0  0  0  0
 21 19  1  0  0  0  0
 22  7  1  0  0  0  0
 23  9  1  0  0  0  0
 24 11  1  0  0  0  0
 25 12  1  0  0  0  0
 26 13  1  0  0  0  0
 27 17  1  0  0  0  0
 28 18  1  0  0  0  0
 29 19  1  0  0  0  0
 30 14  1  0  0  0  0
 30 20  1  0  0  0  0
 31 15  1  0  0  0  0
 31 21  1  0  0  0  0
 32 16  1  0  0  0  0
 32 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0048948

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC(O)=CC3=C2CC(O)C(O3)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O

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

> <INCHI_KEY>
ZESJTWVSXGZYTD-UHFFFAOYSA-N

> <FORMULA>
C21H24O11

> <MOLECULAR_WEIGHT>
452.4087

> <EXACT_MASS>
452.13186161

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
44.0020449294302

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.57

> <JCHEM_LOGP>
-0.47296107800000037

> <ALOGPS_LOGS>
-2.32

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.815378006335113

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.084781510989501

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810923449361297

> <JCHEM_POLAR_SURFACE_AREA>
189.52999999999997

> <JCHEM_REFRACTIVITY>
106.14409999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.14e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0048948 (Catechin 5-glucoside)
Download
PDB for NP0048948 (Catechin 5-glucoside)
HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
CONECT    1    2    8                                                       
CONECT    2    1   11                                                       
CONECT    3    8   12                                                       
CONECT    4    9   14                                                       
CONECT    5    9   15                                                       
CONECT    6   10   13                                                       
CONECT    7   16   22                                                       
CONECT    8    1    3   20                                                  
CONECT    9    4    5   23                                                  
CONECT   10    6   14   15                                                  
CONECT   11    2   12   24                                                  
CONECT   12    3   11   25                                                  
CONECT   13    6   20   26                                                  
CONECT   14    4   10   30                                                  
CONECT   15    5   10   31                                                  
CONECT   16    7   17   32                                                  
CONECT   17   16   18   27                                                  
CONECT   18   17   19   28                                                  
CONECT   19   18   21   29                                                  
CONECT   20    8   13   30                                                  
CONECT   21   19   31   32                                                  
CONECT   22    7                                                            
CONECT   23    9                                                            
CONECT   24   11                                                            
CONECT   25   12                                                            
CONECT   26   13                                                            
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29   19                                                            
CONECT   30   14   20                                                       
CONECT   31   15   21                                                       
CONECT   32   16   21                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

Download
3D PDB for NP0048948 (Catechin 5-glucoside)
Download
SMILES for NP0048948 (Catechin 5-glucoside)
OCC1OC(OC2=CC(O)=CC3=C2CC(O)C(O3)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O
Download
INCHI for NP0048948 (Catechin 5-glucoside)
InChI=1S/C21H24O11/c22-7-16-17(27)18(28)19(29)21(32-16)31-15-5-9(23)4-14-10(15)6-13(26)20(30-14)8-1-2-11(24)12(25)3-8/h1-5,13,16-29H,6-7H2
Download
View in JSmol
Synonyms
ValueSource
(+)-Catechin-5-O-beta-D-glucopyranosideHMDB
Chemical FormulaC21H24O11
Average Mass452.4087 Da
Monoisotopic Mass452.13186 Da
IUPAC Name2-{[2-(3,4-dihydroxyphenyl)-3,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-{[2-(3,4-dihydroxyphenyl)-3,7-dihydroxy-3,4-dihydro-2H-1-benzopyran-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number88126-53-8
SMILES
OCC1OC(OC2=CC(O)=CC3=C2CC(O)C(O3)C2=CC(O)=C(O)C=C2)C(O)C(O)C1O
InChI Identifier
InChI=1S/C21H24O11/c22-7-16-17(27)18(28)19(29)21(32-16)31-15-5-9(23)4-14-10(15)6-13(26)20(30-14)8-1-2-11(24)12(25)3-8/h1-5,13,16-29H,6-7H2
InChI KeyZESJTWVSXGZYTD-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Davallia griffithianaPlant
Davallia mariesiiPlant
Hypericum erectumPlant
Polygonum cuspidatumPlant
Rheum rhabarbarumFooDB
Rheum sp.Plant
Rheum spp.Plant
Chemical Taxonomy
Description Belongs to the class of organic compounds known as flavonoid o-glycosides. Flavonoid O-glycosides are compounds containing a carbohydrate moiety which is O-glycosidically linked to the 2-phenylchromen-4-one flavonoid backbone.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentFlavonoid O-glycosides  
Alternative Parents
Substituents
  • Flavonoid-5-o-glycoside
    • 

  • Flavonoid o-glycoside
    • 

  • Catechin
    • 

  • 3'-hydroxyflavonoid
    • 

  • 3-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • Flavan-3-ol
    • 

  • Hydroxyflavonoid
    • 

  • Flavan
    • 

  • Phenolic glycoside
    • 

  • 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-0.57ALOGPS
logP-0.47ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)9.08ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count11ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area189.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity106.14 m³·mol⁻¹ChemAxon
Polarizability44 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0037948  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB017119  
KNApSAcK IDC00008846  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14345560  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available