NP-MRD: Showing NP-Card for (+)-epicatechin (NP0293910)

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Record Information

Version

2.0

Created at

2022-09-10 02:11:01 UTC

Updated at

2022-09-10 02:11:02 UTC

NP-MRD ID

NP0293910

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-epicatechin

Description

(+)-Epicatechin, also known as ent-epicatechin or catechin C, belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol (+)-Epicatechin is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (+)-Epicatechin has been detected, but not quantified in, several different foods, such as asian pears, star fruits, common buckwheats, pears, and apples. This could make (+)-epicatechin a potential biomarker for the consumption of these foods. (+)-epicatechin is found in Alpinia zerumbet, Averrhoa carambola, Byrsonima crassifolia, Chrysophyllum perpulchrum, Paullinia cupana, Pavetta owariensis, Pseudocedrela kotschyi, Rosa laevigata and Vauquelinia corymbosa. A catechin that is flavan carrying five hydroxy substituents at positions 3, 3', 4', 5 and 7 (the 2S,3S-stereoisomer).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 37  0  0  0  0  0  0  0  0999 V2000
    4.8060   -2.3246    0.9559 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9173   -1.3749    0.5058 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3996   -0.1013    0.2070 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5646    0.9009   -0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1226    2.1606   -0.5301 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2333    0.6504   -0.4155 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7497   -0.6051   -0.1224 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5848   -1.6065    0.3336 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4250   -0.8888   -0.2773 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4641    0.0819   -0.7983 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8304   -0.1976   -0.3214 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3009   -1.5091   -0.3548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5613   -1.8383    0.0739 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3938   -0.8549    0.5524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6900   -1.1414    1.0017 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9649    0.4440    0.5997 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7955    1.4676    1.0840 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6764    0.7684    0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0661    1.4660   -0.3669 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1660    1.6720    0.9821 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3294    1.7206   -0.9051 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5079   -3.2592    1.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4557    0.1226    0.3312 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1050    2.3289   -0.4023 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1821   -2.5844    0.5572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4067    0.0170   -1.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6370   -2.2823   -0.7346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9286   -2.8709    0.0464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0116   -2.1069    0.9677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4720    2.4102    1.1137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3452    1.8055    0.2013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7295    2.1972   -0.9037 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1125    0.9355    1.5467 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2519    1.6608   -2.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6927    2.7364   -0.6644 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  1  0
 19 21  1  0
 21  6  1  0
  6  4  2  0
  4  5  1  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2  8  1  0
  8  7  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 18  2  0
 18 16  1  0
 16 17  1  0
 16 14  2  0
 14 15  1  0
 14 13  1  0
 13 12  2  0
 10 19  1  0
 12 11  1  0
  7  6  1  0
 20 33  1  0
 19 32  1  6
 21 34  1  0
 21 35  1  0
  5 24  1  0
  3 23  1  0
  1 22  1  0
  8 25  1  0
 10 26  1  6
 18 31  1  0
 17 30  1  0
 15 29  1  0
 13 28  1  0
 12 27  1  0
M  END


  Mrv1652307201900052D          

 21 23  0  0  0  0            999 V2000
   -2.8635   -0.2891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8647   -1.1162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1499   -1.5290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1518    0.1235    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4367   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4333   -1.1137    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7182   -1.5226    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0019   -1.1078    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0053   -0.2795    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7250    0.1338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7076    0.1349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4221   -0.2775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1347    0.1362    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1326    0.9620    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4120    1.3720    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7024    0.9557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8500   -0.2740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8449    1.3774    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7134   -1.5184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1494   -2.3539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5779    0.1231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  0  0  0  0
  1 21  1  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3 20  1  0  0  0  0
  3  6  2  0  0  0  0
  5  4  2  0  0  0  0
  5 10  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 19  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  1  0  0  0
 16 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 17  1  0  0  0  0
 13 14  2  0  0  0  0
 14 18  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0293910

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m0/s1

> <INCHI_KEY>
PFTAWBLQPZVEMU-ZFWWWQNUSA-N

> <FORMULA>
C15H14O6

> <MOLECULAR_WEIGHT>
290.2681

> <EXACT_MASS>
290.07903818

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
28.38679947484899

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

> <ALOGPS_LOGP>
1.02

> <JCHEM_LOGP>
1.795107015333333

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.624022697297178

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.004573813837975

> <JCHEM_PKA_STRONGEST_BASIC>
-3.289719332242856

> <JCHEM_POLAR_SURFACE_AREA>
110.38000000000001

> <JCHEM_REFRACTIVITY>
73.9997

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.45e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
l-epicatechin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUL-19         0                                  
HETATM    1  C   UNK     0      -5.345  -0.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.347  -2.084   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.013  -2.854   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.017   0.231   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.682  -0.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.675  -2.079   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.341  -2.842   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.004  -2.068   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.010  -0.522   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.353   0.250   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.321   0.252   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.655  -0.518   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.985   0.254   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.981   1.796   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.636   2.561   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.311   1.784   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.320  -0.511   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       5.310   2.571   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.332  -2.834   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -4.012  -4.394   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -6.679   0.230   0.000  0.00  0.00           O+0
CONECT    1    4   21    2                                                  
CONECT    2    1    3                                                       
CONECT    3    2   20    6                                                  
CONECT    4    1    5                                                       
CONECT    5    4   10    6                                                  
CONECT    6    3    5    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7   19    9                                                  
CONECT    9    8   10   11                                                  
CONECT   10    5    9                                                       
CONECT   11    9   16   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   17   14                                                  
CONECT   14   13   18   15                                                  
CONECT   15   14   16                                                       
CONECT   16   11   15                                                       
CONECT   17   13                                                            
CONECT   18   14                                                            
CONECT   19    8                                                            
CONECT   20    3                                                            
CONECT   21    1                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S)-3',4',5,7-Tetrahydroxyflavan-3-ol	ChEBI
(2S,3S)-3,3',4',5,7-Pentahydroxyflavan	ChEBI
ent-Epicatechin	ChEBI
(+)-cis-3,3',4',5,7-Pentahydroxyflavan	HMDB
(+)-Epicatechol	HMDB
(2S,3S)-(+)-Epicatechin	HMDB
(2S-cis)-2-(3,4-Dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol	HMDB
Catechin C	HMDB
D-Epicatechin	HMDB

Chemical Formula

C₁₅H₁₄O₆

Average Mass

290.2681 Da

Monoisotopic Mass

290.07904 Da

IUPAC Name

(2S,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol

Traditional Name

l-epicatechin

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C15H14O6/c16-8-4-11(18)9-6-13(20)15(21-14(9)5-8)7-1-2-10(17)12(19)3-7/h1-5,13,15-20H,6H2/t13-,15-/m0/s1

InChI Key

PFTAWBLQPZVEMU-ZFWWWQNUSA-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
Alpinia zerumbet	LOTUS Database	35616633
Averrhoa carambola	LOTUS Database	35616633
Byrsonima crassifolia	LOTUS Database	35616633
Gambeya perpulchra	LOTUS Database	35616633
Paullinia cupana	LOTUS Database	35616633
Pavetta owariensis	LOTUS Database	35616633
Pseudocedrela kotschyi	LOTUS Database	35616633
Rosa laevigata	LOTUS Database	35616633
Vauquelinia corymbosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechins. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Catechins

Alternative Parents

Substituents

Catechin
3'-hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Chromane
Benzopyran
1-benzopyran
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Polyol
Ether
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

polyphenol (CHEBI:76125 )
catechin (CHEBI:76125 )
Flavans, Flavanols and Leucoanthocyanidins (C09728 )
Flavan 3-ols (C09728 )
Condensed tannins (Proanthocyanidins) (C09728 )

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	1.02	ALOGPS
logP	1.8	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	9	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	110.38 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	74 m³·mol⁻¹	ChemAxon
Polarizability	28.39 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon