NP-MRD: Showing NP-Card for afzelechin (NP0301629)

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Record Information

Version

2.0

Created at

2022-09-10 14:42:49 UTC

Updated at

2022-09-10 14:42:49 UTC

NP-MRD ID

NP0301629

Secondary Accession Numbers

None

Natural Product Identification

Common Name

afzelechin

Description

afzelechin is found in Senegalia polyacantha, Actinidia chinensis, Artocarpus fretessii, Bergenia pacumbis, Cassia abbreviata, Cassipourea gummiflua, Hovenia dulcis, Kandelia candel, Pinalia floribunda, Prunus persica, Rhizophora stylosa, Typha capensis, Typha latifolia and Wisteria floribunda. afzelechin was first documented in 2008 (PMID: 18622126).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 36  0  0  0  0  0  0  0  0999 V2000
    6.0247   -0.7598    0.8193 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6627   -0.7190    0.5195 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1375   -1.3018   -0.6180 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7776   -1.2301   -0.8646 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9007   -0.5919   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4656   -0.5490   -0.3291 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3486   -0.8449    0.7939 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7097   -0.6662    0.6455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6357   -1.3434    1.4193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9940   -1.1857    1.2933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9159   -1.8704    2.0754 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4483   -0.2999    0.3385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5537    0.4032   -0.4627 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0281    1.2877   -1.4163 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1711    0.2107   -0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2967    1.0000   -1.1913 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1431    0.8670   -0.7967 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9690    1.1198   -1.8996 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4304   -0.0096    1.1249 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7958   -0.0742    1.3850 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6531   -1.2342    0.1800 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8363   -1.7992   -1.2776 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3781   -1.6956   -1.7677 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2278   -1.2511   -1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2480   -2.0290    2.1571 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1897   -1.4155    2.9408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5332   -0.1660    0.2291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3707    1.7830   -1.9857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5599    2.0860   -1.1319 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4341    0.6506   -2.2540 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4187    1.5376    0.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6581    0.5360   -2.6373 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7676    0.5068    1.8266 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1906    0.3959    2.2947 H   0  0  0  0  0  0  0  0  0  0  0  0
 17 18  1  0
 17 16  1  0
 16 15  1  0
 15 13  2  0
 13 14  1  0
 13 12  1  0
 12 10  2  0
 10 11  1  0
 10  9  1  0
  9  8  2  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  4  3  1  0
  3  2  2  0
  2  1  1  0
  2 20  1  0
 20 19  2  0
  6 17  1  0
 19  5  1  0
  8 15  1  0
 17 31  1  1
 18 32  1  0
 16 29  1  0
 16 30  1  0
 14 28  1  0
 12 27  1  0
 11 26  1  0
  9 25  1  0
  6 24  1  6
  4 23  1  0
  3 22  1  0
  1 21  1  0
 20 34  1  0
 19 33  1  0
M  END


  Mrv1652307301920052D          

 22 24  0  0  1  0            999 V2000
    4.2868   -2.4750    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
    5.0013   -2.8875    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
    0.7145   -0.4125    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
    2.8579    0.0000    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
    5.7158   -2.4750    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
    1.4289    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  1  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
    3.5724   -1.2375    0.0000 C   0  0  2  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
    0.0000   -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
    4.2868    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
    4.2868   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.0625    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  8  1  2  0  0  0  0
  8  2  1  0  0  0  0
  9  3  2  0  0  0  0
  9  4  1  0  0  0  0
 10  5  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  5  1  0  0  0  0
 12 11  2  0  0  0  0
 13  7  1  0  0  0  0
 14  6  2  0  0  0  0
 14 11  1  0  0  0  0
 15  8  1  0  0  0  0
 13 15  1  0  0  0  0
 16  9  1  0  0  0  0
 17 10  1  0  0  0  0
 18 12  1  0  0  0  0
 13 19  1  0  0  0  0
 20 14  1  0  0  0  0
 15 20  1  0  0  0  0
 13 21  1  1  0  0  0
 15 22  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0301629

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C15H14O5/c16-9-3-1-8(2-4-9)15-13(19)7-11-12(18)5-10(17)6-14(11)20-15/h1-6,13,15-19H,7H2/t13-,15+/m0/s1

> <INCHI_KEY>
RSYUFYQTACJFML-DZGCQCFKSA-N

> <FORMULA>
C15H14O5

> <MOLECULAR_WEIGHT>
274.272

> <EXACT_MASS>
274.084123551

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
27.68859957154885

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <JCHEM_LOGP>
2.098672337

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.732353999322413

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.149760394668172

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2843440587393635

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
72.01880000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
afzelechin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         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  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.669  -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       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   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      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   0.000   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       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       8.002  -1.540   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       6.668  -3.850   0.000  0.00  0.00           H+0
CONECT    1    3    8                                                       
CONECT    2    4    8                                                       
CONECT    3    1    9                                                       
CONECT    4    2    9                                                       
CONECT    5   10   12                                                       
CONECT    6   10   14                                                       
CONECT    7   11   13                                                       
CONECT    8    1    2   15                                                  
CONECT    9    3    4   16                                                  
CONECT   10    5    6   17                                                  
CONECT   11    7   12   14                                                  
CONECT   12    5   11   18                                                  
CONECT   13    7   15   19   21                                             
CONECT   14    6   11   20                                                  
CONECT   15    8   13   20   22                                             
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   12                                                            
CONECT   19   13                                                            
CONECT   20   14   15                                                       
CONECT   21   13                                                            
CONECT   22   15                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Value	Source
(+)-Afzelechin	ChEBI
3,5,7,4'-Tetrahydroxyflavan	ChEBI
(2R,3R)-2-(4-Hydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol	MeSH

Chemical Formula

C₁₅H₁₄O₅

Average Mass

274.2720 Da

Monoisotopic Mass

274.08412 Da

IUPAC Name

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

Traditional Name

afzelechin

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C15H14O5/c16-9-3-1-8(2-4-9)15-13(19)7-11-12(18)5-10(17)6-14(11)20-15/h1-6,13,15-19H,7H2/t13-,15+/m0/s1

InChI Key

RSYUFYQTACJFML-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
Acacia polyacantha	LOTUS Database	35616633
Actinidia chinensis	LOTUS Database	35616633
Artocarpus fretessii	LOTUS Database	35616633
Bergenia pacumbis	LOTUS Database	35616633
Cassia abbreviata	LOTUS Database	35616633
Cassipourea gummiflua	LOTUS Database	35616633
Hovenia dulcis	LOTUS Database	35616633
Kandelia candel	LOTUS Database	35616633
Pinalia floribunda	LOTUS Database	35616633
Prunus persica	LOTUS Database	35616633
Rhizophora stylosa	LOTUS Database	35616633
Typha capensis	LOTUS Database	35616633
Typha latifolia	LOTUS Database	35616633
Wisteria floribunda	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavan-3-ols. These are flavans that bear and hydroxyl group at position 3 (B ring), but not at position 4.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Flavan-3-ols

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

catechin (CHEBI:2507 )
tetrahydroxyflavan (CHEBI:2507 )
Flavans, Flavanols and Leucoanthocyanidins (C09320 )
Flavan 3-ols (C09320 )
Flavans, Flavanols and Leucoanthocyanidins (LMPK12020035 )

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	2.1	ChemAxon
pKa (Strongest Acidic)	9.15	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	72.02 m³·mol⁻¹	ChemAxon
Polarizability	27.69 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

FDB002779

KNApSAcK ID

C00000937

Chemspider ID

Not Available

KEGG Compound ID

C09320

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Afzelechin

METLIN ID

Not Available

PubChem Compound

442154

PDB ID

Not Available

ChEBI ID

2507

Good Scents ID

Not Available

References

General References

Saijyo J, Suzuki Y, Okuno Y, Yamaki H, Suzuki T, Miyazawa M: Alpha-glucosidase inhibitor from Bergenia ligulata. J Oleo Sci. 2008;57(8):431-5. doi: 10.5650/jos.57.431. [PubMed:18622126 ]
Feng HL, Tian L, Chai WM, Chen XX, Shi Y, Gao YS, Yan CL, Chen QX: Isolation and purification of condensed tannins from flamboyant tree and their antioxidant and antityrosinase activities. Appl Biochem Biotechnol. 2014 May;173(1):179-92. doi: 10.1007/s12010-014-0828-z. Epub 2014 Mar 27. [PubMed:24671565 ]
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LOTUS database [Link]

Showing NP-Card for afzelechin (NP0301629)

MOL for NP0301629 (afzelechin)

3D MOL for NP0301629 (afzelechin)

3D SDF for NP0301629 (afzelechin)

3D-SDF for NP0301629 (afzelechin)

PDB for NP0301629 (afzelechin)

3D PDB for NP0301629 (afzelechin)

SMILES for NP0301629 (afzelechin)

INCHI for NP0301629 (afzelechin)

Structure for NP0301629 (afzelechin)

3D Structure for NP0301629 (afzelechin)