NP-MRD: Showing NP-Card for (2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0218499)

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Record Information

Version

2.0

Created at

2022-09-05 19:11:09 UTC

Updated at

2022-09-05 19:11:09 UTC

NP-MRD ID

NP0218499

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

SCHEMBL20767636 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. (2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol is found in Podocarpus fasciculus. Based on a literature review very few articles have been published on SCHEMBL20767636.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
    4.7063    1.4263    2.4789 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9402    0.7289    1.5356 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5362   -0.0581    0.5768 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7018   -0.7226   -0.3275 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2819   -1.5145   -1.2926 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3199   -0.6052   -0.2759 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7609    0.1988    0.7051 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5541    0.8586    1.6012 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3637    0.3114    0.7435 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3707    0.3456   -0.4886 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8108    0.2337   -0.1919 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7422   -0.3825   -1.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0809   -0.4263   -0.6753 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0234   -1.0495   -1.5171 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5729    0.1166    0.4783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9370    0.0454    0.7848 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6677    0.7279    1.3090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3327    0.7859    0.9868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4211    1.4111    1.8398 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1788   -0.5073   -1.5539 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5341    0.2548   -2.6866 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4142   -1.3074   -1.1881 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2680    2.0035    3.1817 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6071   -0.1331    0.5583 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2704   -1.6062   -1.3429 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0850    1.4792    2.3600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1939    1.4270   -0.8410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4297   -0.8214   -1.9467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6875   -1.4525   -2.3703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3070    0.4428    1.6411 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0563    1.1644    2.2370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7589    1.8177    2.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5663   -1.2377   -1.9375 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3437   -0.1208   -3.1280 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9619   -1.5136   -2.1325 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1304   -2.3210   -0.8030 H   0  0  0  0  0  0  0  0  0  0  0  0
 21 20  1  0
 20 22  1  0
 22  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 12  2  0
 12 13  1  0
 13 14  1  0
 13 15  2  0
 15 16  1  0
 15 17  1  0
 17 18  2  0
 18 19  1  0
 10 20  1  0
 18 11  1  0
  7  6  1  0
 21 34  1  0
 20 33  1  6
 22 35  1  0
 22 36  1  0
  5 25  1  0
  3 24  1  0
  1 23  1  0
  8 26  1  0
 10 27  1  6
 12 28  1  0
 14 29  1  0
 16 30  1  0
 17 31  1  0
 19 32  1  0
M  END


  Mrv1652309052221112D          

 22 24  0  0  1  0            999 V2000
   -1.4289    0.0000    0.0000 O   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
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   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   -1.2375    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
    0.0000   -0.0000    0.0000 C   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
    2.1434   -0.4125    0.0000 C   0  0  2  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
    2.8579    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
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.8250    0.0000 C   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
    4.2868   -0.0000    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
    3.5724   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  1  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   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  2  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  0  0  0  0
 10 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
  6 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0218499

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1CC2=C(O)C=C(O)C=C2O[C@@H]1C1=CC(O)=C(O)C=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O7/c16-6-1-9(17)7-3-13(21)15(22-14(7)2-6)8-4-11(19)12(20)5-10(8)18/h1-2,4-5,13,15-21H,3H2/t13-,15+/m0/s1

> <INCHI_KEY>
UVDNRKMZMPBBTJ-DZGCQCFKSA-N

> <FORMULA>
C15H14O7

> <MOLECULAR_WEIGHT>
306.27

> <EXACT_MASS>
306.073952791

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
28.89146891036944

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
1.4915416936666661

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.58867032442982

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.983941149117756

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3097479612712926

> <JCHEM_POLAR_SURFACE_AREA>
130.61

> <JCHEM_REFRACTIVITY>
75.98060000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   22                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    2                                                       
CONECT    9    7   10                                                       
CONECT   10    9   11   20                                                  
CONECT   11   10   12   18                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   11   19                                                  
CONECT   19   18                                                            
CONECT   20   10   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    6                                                       
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₄O₇

Average Mass

306.2700 Da

Monoisotopic Mass

306.07395 Da

IUPAC Name

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

Traditional Name

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

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=C1O

InChI Identifier

InChI=1S/C15H14O7/c16-6-1-9(17)7-3-13(21)15(22-14(7)2-6)8-4-11(19)12(20)5-10(8)18/h1-2,4-5,13,15-21H,3H2/t13-,15+/m0/s1

InChI Key

UVDNRKMZMPBBTJ-DZGCQCFKSA-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
Podocarpus fasciculus	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
Hydroxyquinol derivative
Phenol
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Secondary alcohol
Polyol
Oxacycle
Ether
Organoheterocyclic compound
Organooxygen compound
Alcohol
Organic oxygen compound
Hydrocarbon derivative
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	1.49	ChemAxon
pKa (Strongest Acidic)	8.98	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	130.61 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	75.98 m³·mol⁻¹	ChemAxon
Polarizability	28.89 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

137521409

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol (NP0218499)

MOL for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D MOL for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D SDF for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D-SDF for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

PDB for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D PDB for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

SMILES for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

INCHI for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

Structure for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)

3D Structure for NP0218499 ((2r,3s)-2-(2,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3,5,7-triol)