NP-MRD: Showing NP-Card for Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate (NP0056127)

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Record Information

Version

2.0

Created at

2022-04-28 01:59:56 UTC

Updated at

2022-04-28 01:59:56 UTC

NP-MRD ID

NP0056127

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate

Description

Epigallocatechin 5,3',5'-trimethyl ether 3-o-gallate belongs to the class of organic compounds known as catechin gallates. These are organic compounds containing a gallate moiety glycosidically linked to a catechin. Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate is found in Sedum crassularia and Sedum sediforme . Based on a literature review very few articles have been published on Epigallocatechin 5,3',5'-trimethyl ether 3-o-gallate.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652304282203592D          

 36 39  0  0  1  0            999 V2000
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    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END

  Mrv1652304282203592D          

 36 39  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0056127

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC(O)=CC(OC)=C2C[C@H]1OC(=O)C1=CC(O)=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H24O11/c1-32-17-8-13(26)9-18-14(17)10-21(36-25(31)12-4-15(27)22(29)16(28)5-12)24(35-18)11-6-19(33-2)23(30)20(7-11)34-3/h4-9,21,24,26-30H,10H2,1-3H3/t21-,24-/m1/s1

> <INCHI_KEY>
SMSODIBAMOCYJH-ZJSXRUAMSA-N

> <FORMULA>
C25H24O11

> <MOLECULAR_WEIGHT>
500.456

> <EXACT_MASS>
500.131861593

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
49.3981192293538

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-7-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

> <ALOGPS_LOGP>
3.00

> <JCHEM_LOGP>
3.5138277453333338

> <ALOGPS_LOGS>
-4.41

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.080147935597765

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.057828152755315

> <JCHEM_PKA_STRONGEST_BASIC>
-4.411841040830681

> <JCHEM_POLAR_SURFACE_AREA>
164.37

> <JCHEM_REFRACTIVITY>
125.1922

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.96e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-7-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

> <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  -4.620   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      10.669  -0.000   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   36                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   34                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   23                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   22                                                  
CONECT   17   16   18   21                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18   14                                                       
CONECT   20   18                                                            
CONECT   21   17                                                            
CONECT   22   16                                                            
CONECT   23    8   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   27   31                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   23                                                       
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31   26                                                            
CONECT   32   25   33                                                       
CONECT   33   32                                                            
CONECT   34    3   35                                                       
CONECT   35   34                                                            
CONECT   36    1                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Value	Source
Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallic acid	Generator

Chemical Formula

C₂₅H₂₄O₁₁

Average Mass

500.4560 Da

Monoisotopic Mass

500.13186 Da

IUPAC Name

(2R,3R)-7-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

Traditional Name

(2R,3R)-7-hydroxy-2-(4-hydroxy-3,5-dimethoxyphenyl)-5-methoxy-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC(OC)=C1O)[C@H]1OC2=CC(O)=CC(OC)=C2C[C@H]1OC(=O)C1=CC(O)=C(O)C(O)=C1

InChI Identifier

InChI=1S/C25H24O11/c1-32-17-8-13(26)9-18-14(17)10-21(36-25(31)12-4-15(27)22(29)16(28)5-12)24(35-18)11-6-19(33-2)23(30)20(7-11)34-3/h4-9,21,24,26-30H,10H2,1-3H3/t21-,24-/m1/s1

InChI Key

SMSODIBAMOCYJH-ZJSXRUAMSA-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
Sedum crassularia	LOTUS Database	35616633
Sedum sediforme	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as catechin gallates. These are organic compounds containing a gallate moiety glycosidically linked to a catechin.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavans

Direct Parent

Catechin gallates

Alternative Parents

Substituents

Catechin gallate
Epigallocatechin
3p-methoxyflavonoid-skeleton
5-methoxyflavonoid-skeleton
4'-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Galloyl ester
Gallic acid or derivatives
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Methoxyphenol
Benzoate ester
1-benzopyran
Dimethoxybenzene
Benzopyran
M-dimethoxybenzene
Chromane
Pyrogallol derivative
Benzoic acid or derivatives
Benzenetriol
Phenoxy compound
Anisole
Methoxybenzene
Benzoyl
Phenol ether
Alkyl aryl ether
Phenol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Monocyclic benzene moiety
Carboxylic acid ester
Carboxylic acid derivative
Ether
Polyol
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Flavans, Flavanols and Leucoanthocyanidins (LMPK12020140 )

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	3	ALOGPS
logP	3.51	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	8.06	ChemAxon
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	164.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	125.19 m³·mol⁻¹	ChemAxon
Polarizability	49.4 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

C00008893

Chemspider ID

24842578

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44257124

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate (NP0056127)

MOL for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

3D MOL for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

3D SDF for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

3D-SDF for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

PDB for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

3D PDB for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

SMILES for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

INCHI for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

Structure for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)

3D Structure for NP0056127 (Epigallocatechin 5,3',5'-trimethyl ether 3-O-gallate)