NP-MRD: Showing NP-Card for Catechin 5,3'-di-O-beta-D-glucopyranoside (NP0056098)

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Record Information

Version

2.0

Created at

2022-04-28 01:58:47 UTC

Updated at

2022-04-28 01:58:47 UTC

NP-MRD ID

NP0056098

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Catechin 5,3'-di-O-beta-D-glucopyranoside

Description

(2S,3R,4S,5S,6R)-2-{[(2R,3S)-3,7-dihydroxy-2-(4-hydroxy-3-{[(2S,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-3,4-dihydro-2H-1-benzopyran-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol 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 5,3'-di-O-beta-D-glucopyranoside is found in Rheum sp. and Rheum spp.. Based on a literature review very few articles have been published on (2S,3R,4S,5S,6R)-2-{[(2R,3S)-3,7-dihydroxy-2-(4-hydroxy-3-{[(2S,3S,4S,5S,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-3,4-dihydro-2H-1-benzopyran-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282203582D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282203582D          

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    5.7158    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -0.4125    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
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  2  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
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
  9 11  1  1  0  0  0
  8 12  1  6  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 12 17  1  0  0  0  0
 16 18  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 19 24  1  0  0  0  0
 23 25  1  1  0  0  0
 25 26  1  0  0  0  0
 22 27  1  1  0  0  0
 21 28  1  6  0  0  0
 20 29  1  6  0  0  0
 15 30  1  0  0  0  0
  3 31  1  0  0  0  0
 32 31  1  6  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 32 37  1  0  0  0  0
 36 38  1  6  0  0  0
 38 39  1  0  0  0  0
 35 40  1  1  0  0  0
 34 41  1  6  0  0  0
 33 42  1  1  0  0  0
  1 43  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0056098

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1O[C@@H](OC2=CC(=CC=C2O)[C@H]2OC3=CC(O)=CC(O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)=C3C[C@@H]2O)[C@@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H34O16/c28-7-17-19(33)21(35)23(37)26(42-17)40-15-5-10(30)4-14-11(15)6-13(32)25(39-14)9-1-2-12(31)16(3-9)41-27-24(38)22(36)20(34)18(8-29)43-27/h1-5,13,17-38H,6-8H2/t13-,17+,18-,19+,20+,21-,22-,23+,24-,25+,26+,27+/m0/s1

> <INCHI_KEY>
LCSWUKTXJWVVJX-AGZLOHOJSA-N

> <FORMULA>
C27H34O16

> <MOLECULAR_WEIGHT>
614.553

> <EXACT_MASS>
614.184685015

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
58.01595221437314

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.46

> <JCHEM_LOGP>
-2.7410291713333326

> <ALOGPS_LOGS>
-2.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.021707103297961

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.420584520075332

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483953478845885

> <JCHEM_POLAR_SURFACE_AREA>
268.67999999999995

> <JCHEM_REFRACTIVITY>
138.2885

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.57e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   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       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   43                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   31                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9                                                            
CONECT   12    8   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   30                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21   29                                                  
CONECT   21   20   22   28                                                  
CONECT   22   21   23   27                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23   19                                                       
CONECT   25   23   26                                                       
CONECT   26   25                                                            
CONECT   27   22                                                            
CONECT   28   21                                                            
CONECT   29   20                                                            
CONECT   30   15                                                            
CONECT   31    3   32                                                       
CONECT   32   31   33   37                                                  
CONECT   33   32   34   42                                                  
CONECT   34   33   35   41                                                  
CONECT   35   34   36   40                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36   32                                                       
CONECT   38   36   39                                                       
CONECT   39   38                                                            
CONECT   40   35                                                            
CONECT   41   34                                                            
CONECT   42   33                                                            
CONECT   43    1                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   94    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₄O₁₆

Average Mass

614.5530 Da

Monoisotopic Mass

614.18469 Da

IUPAC Name

(2S,3S,4S,5S,6S)-2-{5-[(2R,3S)-3,7-dihydroxy-5-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydro-2H-1-benzopyran-2-yl]-2-hydroxyphenoxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

CAS Registry Number

Not Available

SMILES

OC[C@@H]1O[C@@H](OC2=CC(=CC=C2O)[C@H]2OC3=CC(O)=CC(O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)=C3C[C@@H]2O)[C@@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C27H34O16/c28-7-17-19(33)21(35)23(37)26(42-17)40-15-5-10(30)4-14-11(15)6-13(32)25(39-14)9-1-2-12(31)16(3-9)41-27-24(38)22(36)20(34)18(8-29)43-27/h1-5,13,17-38H,6-8H2/t13-,17+,18-,19+,20+,21-,22-,23+,24-,25+,26+,27+/m0/s1

InChI Key

LCSWUKTXJWVVJX-AGZLOHOJSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Rheum sp.	Plant	KNApSAcK
Rheum spp.	Plant	KNApSAcK

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.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid O-glycosides

Alternative Parents

Substituents

Flavonoid o-glycoside
Flavonoid-3p-o-glycoside
Flavonoid-5-o-glycoside
Catechin
Hydroxyflavonoid
Flavan-3-ol
7-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
Flavan
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
1-benzopyran
Benzopyran
Chromane
Phenoxy compound
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Alcohol
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	-1.5	ALOGPS
logP	-2.7	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	9.42	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	268.68 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	138.29 m³·mol⁻¹	ChemAxon
Polarizability	58.02 Å³	ChemAxon
Number of Rings	5	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

162909121

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Catechin 5,3'-di-O-beta-D-glucopyranoside (NP0056098)

MOL for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

3D MOL for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

3D SDF for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

3D-SDF for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

PDB for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

3D PDB for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

SMILES for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

INCHI for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

Structure for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)

3D Structure for NP0056098 (Catechin 5,3'-di-O-beta-D-glucopyranoside)