NP-MRD: Showing NP-Card for (3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0324591)

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Record Information

Version

2.0

Created at

2022-09-12 04:45:45 UTC

Updated at

2022-09-12 04:45:45 UTC

NP-MRD ID

NP0324591

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol

Description

(3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol belongs to the class of organic compounds known as catechins. (3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol is found in Vachellia karroo, Arabidopsis thaliana, Diospyros kaki, Litchi chinensis, Prunus armeniaca, Prunus avium and Vitis vinifera. Catechins are compounds containing a catechin moiety, which is a 3,4-dihydro-2-chromene-3,5.7-Tiol (3R)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3,5,7-triol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

(-)Epicatechin
  Mrv1572001071604202D          

 21 23  0  0  1  0            999 V2000
    2.0414   -2.6714    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3269   -2.2589    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6125   -2.6714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1020   -2.2589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8165   -2.6714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8165   -3.4964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5310   -1.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2454   -1.0214    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8165   -1.0214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1020   -1.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6125   -1.0214    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3269   -1.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0414   -1.0214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4703   -0.1964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1848    0.2161    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4703   -1.0214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7559   -1.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1847   -1.4339    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0414   -0.1964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7558    0.2161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5311   -2.2589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  4 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 13 17  2  0  0  0  0
 16 18  1  0  0  0  0
 13 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 14  1  0  0  0  0
 16 17  1  0  0  0  0
  9 10  1  0  0  0  0
  7 21  1  0  0  0  0
 21  5  2  0  0  0  0
  5  4  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0324591

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CC2=C(OC1C1=CC(O)=C(O)C=C1)C=C(O)C=C2O

> <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?/m1/s1

> <INCHI_KEY>
PFTAWBLQPZVEMU-AFYYWNPRSA-N

> <FORMULA>
C15H14O6

> <MOLECULAR_WEIGHT>
290.271

> <EXACT_MASS>
290.079038171

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
28.727443236736793

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-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>
73.99970000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.45e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: (-)Epicatechin                                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  O   UNK     0       3.811  -4.987   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.477  -4.217   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.143  -4.987   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.190  -4.217   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.524  -4.987   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.524  -6.527   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.858  -2.677   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -4.191  -1.907   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.524  -1.907   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.190  -2.677   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.143  -1.907   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.477  -2.677   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.811  -1.907   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.478  -0.367   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.812   0.403   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.478  -1.907   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.144  -2.677   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       7.811  -2.677   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.811  -0.367   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.144   0.403   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.858  -4.217   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3   10    5                                                  
CONECT    5    6   21    4                                                  
CONECT    6    5                                                            
CONECT    7    8    9   21                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    4   11    9                                                  
CONECT   11   10   12                                                       
CONECT   12   11    2   13                                                  
CONECT   13   12   17   19                                                  
CONECT   14   15   16   20                                                  
CONECT   15   14                                                            
CONECT   16   14   18   17                                                  
CONECT   17   13   16                                                       
CONECT   18   16                                                            
CONECT   19   13   20                                                       
CONECT   20   19   14                                                       
CONECT   21    7    5                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   46    0
END

View in JSmol

Synonyms

Value	Source
3,3',4',5,7-Flavanpentol	MeSH
Catechinic acid	MeSH
Cyanidanol 3	MeSH
Cyanidanol-3	MeSH
Catechuic acid	MeSH
(+)-Cyanidanol	MeSH
Catechin	MeSH
Catergen	MeSH
KB-53	MeSH
Zyma	MeSH
(+)-Catechin	MeSH
(+)-Cyanidanol-3	MeSH
(-)-Epicatechin	MeSH
Cianidanol	MeSH
KB 53	MeSH

Chemical Formula

C₁₅H₁₄O₆

Average Mass

290.2710 Da

Monoisotopic Mass

290.07904 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

O[C@@H]1CC2=C(OC1C1=CC(O)=C(O)C=C1)C=C(O)C=C2O

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?/m1/s1

InChI Key

PFTAWBLQPZVEMU-AFYYWNPRSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Acacia karoo	LOTUS Database	35616633
Arabidopsis thaliana	LOTUS Database	35616633
Diospyros kaki	LOTUS Database	35616633
Litchi chinensis	LOTUS Database	35616633
Prunus armeniaca	LOTUS Database	35616633
Prunus avium	LOTUS Database	35616633
Vitis vinifera	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

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	1.02	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	28.73 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

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

255538

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0324591)

MOL for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D MOL for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D SDF for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D-SDF for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

PDB for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D PDB for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

SMILES for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

INCHI for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

Structure for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D Structure for NP0324591 ((3r)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)