NP-MRD: Showing NP-Card for (2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate (NP0206067)

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Record Information

Version

2.0

Created at

2022-09-05 02:09:38 UTC

Updated at

2022-09-05 02:09:38 UTC

NP-MRD ID

NP0206067

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

Description

(2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate belongs to the class of organic compounds known as catechin gallates. These are organic compounds containing a gallate moiety glycosidically linked to a catechin. (2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate is found in Diospyros kaki. Based on a literature review very few articles have been published on (2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052204092D          

 41 45  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052204092D          

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  4  5  1  0  0  0  0
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  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
  5 14  1  0  0  0  0
 14 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
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 14 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  4 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  2  0  0  0  0
 24 32  1  0  0  0  0
  2 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 35 37  2  0  0  0  0
 37 38  1  0  0  0  0
 37 39  1  0  0  0  0
 39 40  1  0  0  0  0
 39 41  2  0  0  0  0
 33 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0206067

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1=CC(O)=C2[C@H](SCC3=CC=CC=C3)[C@@H](OC(=O)C3=CC(O)=C(O)C(O)=C3)[C@H](OC2=C1)C1=CC(O)=C(O)C(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C29H24O11S/c30-16-10-17(31)23-22(11-16)39-26(14-6-18(32)24(36)19(33)7-14)27(28(23)41-12-13-4-2-1-3-5-13)40-29(38)15-8-20(34)25(37)21(35)9-15/h1-11,26-28,30-37H,12H2/t26-,27+,28+/m1/s1

> <INCHI_KEY>
CEUGTIORABEACS-PKTNWEFCSA-N

> <FORMULA>
C29H24O11S

> <MOLECULAR_WEIGHT>
580.56

> <EXACT_MASS>
580.103932767

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
56.44399614084328

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

> <JCHEM_LOGP>
5.234491494999999

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.692233696859498

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.985250512261797

> <JCHEM_PKA_STRONGEST_BASIC>
-5.424508612613274

> <JCHEM_POLAR_SURFACE_AREA>
197.36999999999998

> <JCHEM_REFRACTIVITY>
148.4204

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

> <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       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0       2.667   1.540   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -5.335   1.540   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -2.667   6.160   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   23                                                  
CONECT    5    4    6   14                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14    5   15   21                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   14   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22    4   24                                                  
CONECT   24   23   25   32                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   24                                                       
CONECT   33    2   34   41                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   33                                                       
MASTER        0    0    0    0    0    0    0    0   41    0   90    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S,4S)-4-(Benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoic acid	Generator
(2R,3S,4S)-4-(Benzylsulphanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate	Generator
(2R,3S,4S)-4-(Benzylsulphanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoic acid	Generator

Chemical Formula

C₂₉H₂₄O₁₁S

Average Mass

580.5600 Da

Monoisotopic Mass

580.10393 Da

IUPAC Name

(2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

Traditional Name

(2R,3S,4S)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2H-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

OC1=CC(O)=C2[C@H](SCC3=CC=CC=C3)[C@@H](OC(=O)C3=CC(O)=C(O)C(O)=C3)[C@H](OC2=C1)C1=CC(O)=C(O)C(O)=C1

InChI Identifier

InChI=1S/C29H24O11S/c30-16-10-17(31)23-22(11-16)39-26(14-6-18(32)24(36)19(33)7-14)27(28(23)41-12-13-4-2-1-3-5-13)40-29(38)15-8-20(34)25(37)21(35)9-15/h1-11,26-28,30-37H,12H2/t26-,27+,28+/m1/s1

InChI Key

CEUGTIORABEACS-PKTNWEFCSA-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
Diospyros kaki	LOTUS Database	35616633

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
3'-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Galloyl ester
Gallic acid or derivatives
P-hydroxybenzoic acid alkyl ester
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Benzopyran
Chromane
Benzoate ester
1-benzopyran
Pyrogallol derivative
Benzoic acid or derivatives
Benzenetriol
Benzoyl
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Dialkylthioether
Sulfenyl compound
Thioether
Polyol
Ether
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organosulfur compound
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Organic oxide
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	5.23	ChemAxon
pKa (Strongest Acidic)	7.99	ChemAxon
pKa (Strongest Basic)	-5.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	197.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	148.42 m³·mol⁻¹	ChemAxon
Polarizability	56.44 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	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

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

162946614

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,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate (NP0206067)

MOL for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

3D MOL for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

3D SDF for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

3D-SDF for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

PDB for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

3D PDB for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

SMILES for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

INCHI for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

Structure for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)

3D Structure for NP0206067 ((2r,3s,4s)-4-(benzylsulfanyl)-5,7-dihydroxy-2-(3,4,5-trihydroxyphenyl)-3,4-dihydro-2h-1-benzopyran-3-yl 3,4,5-trihydroxybenzoate)