NP-MRD: Showing NP-Card for (-)-Seguinoside E (NP0077740)

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Record Information

Version

2.0

Created at

2022-04-28 22:54:06 UTC

Updated at

2022-04-28 22:54:06 UTC

NP-MRD ID

NP0077740

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Seguinoside E

Description

[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. (-)-Seguinoside E is found in Myrsine seguinii. Based on a literature review very few articles have been published on [(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292200542D          

 39 42  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292200542D          

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  6  7  1  1  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
 11 14  1  0  0  0  0
  4 15  1  1  0  0  0
 15 16  1  0  0  0  0
  3 17  1  6  0  0  0
  2 18  1  1  0  0  0
  1 19  1  6  0  0  0
 20 19  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 20 24  1  0  0  0  0
 24 25  1  1  0  0  0
 23 26  1  1  0  0  0
 23 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
 33 38  1  0  0  0  0
 38 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0077740

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC(=C1)C(=O)OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]2OC2=CC=C(O)C=C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O14/c1-34-16-8-12(2-7-15(16)28)22(32)35-10-25(33)11-36-24(21(25)31)39-20-19(30)18(29)17(9-26)38-23(20)37-14-5-3-13(27)4-6-14/h2-8,17-21,23-24,26-31,33H,9-11H2,1H3/t17-,18-,19+,20-,21+,23-,24+,25-/m1/s1

> <INCHI_KEY>
QHRHKYAZXRNVAA-KXQNOTADSA-N

> <FORMULA>
C25H30O14

> <MOLECULAR_WEIGHT>
554.501

> <EXACT_MASS>
554.163555646

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
53.65982124473129

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate

> <ALOGPS_LOGP>
-0.01

> <JCHEM_LOGP>
-0.14438871933333297

> <ALOGPS_LOGS>
-2.64

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.877331982575068

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.931038000965879

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810925692673598

> <JCHEM_POLAR_SURFACE_AREA>
214.05999999999997

> <JCHEM_REFRACTIVITY>
127.10049999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.28e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       6.360  -9.116   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.265 -10.362   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.639 -11.769   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.107 -11.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.202 -10.684   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.828  -9.277   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.923  -8.031   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.391  -8.192   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.765  -9.599   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.234  -9.760   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.672  -8.514   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.045  -7.107   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.486  -6.946   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.203  -8.675   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.481 -13.337   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.949 -13.498   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       7.544 -13.015   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       8.797 -10.201   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       6.986  -7.709   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.081  -6.464   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.541  -6.464   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.065  -4.999   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.311  -4.094   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       6.557  -4.999   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.021  -4.523   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.555  -2.752   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.067  -2.752   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       7.607  -2.736   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       8.363  -1.394   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       7.579  -0.069   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       9.903  -1.378   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.659  -0.036   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      12.199  -0.020   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.983  -1.346   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.227  -2.688   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      10.687  -2.704   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      14.523  -1.330   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      12.955   1.321   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      14.495   1.337   0.000  0.00  0.00           C+0
CONECT    1    2    6   19                                                  
CONECT    2    1    3   18                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5   15                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11                                                            
CONECT   15    4   16                                                       
CONECT   16   15                                                            
CONECT   17    3                                                            
CONECT   18    2                                                            
CONECT   19    1   20                                                       
CONECT   20   19   21   24                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   26   27                                             
CONECT   24   23   20   25                                                  
CONECT   25   24                                                            
CONECT   26   23                                                            
CONECT   27   23   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38   33   39                                                       
CONECT   39   38                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Value	Source
[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoic acid	Generator

Chemical Formula

C₂₅H₃₀O₁₄

Average Mass

554.5010 Da

Monoisotopic Mass

554.16356 Da

IUPAC Name

[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate

Traditional Name

[(3S,4R,5S)-5-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(4-hydroxyphenoxy)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxy-3-methoxybenzoate

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=CC(=C1)C(=O)OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]2OC2=CC=C(O)C=C2)[C@@H]1O

InChI Identifier

InChI=1S/C25H30O14/c1-34-16-8-12(2-7-15(16)28)22(32)35-10-25(33)11-36-24(21(25)31)39-20-19(30)18(29)17(9-26)38-23(20)37-14-5-3-13(27)4-6-14/h2-8,17-21,23-24,26-31,33H,9-11H2,1H3/t17-,18-,19+,20-,21+,23-,24+,25-/m1/s1

InChI Key

QHRHKYAZXRNVAA-KXQNOTADSA-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
Myrsine seguinii	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

Hydrolyzable tannin
Phenolic glycoside
M-methoxybenzoic acid or derivatives
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
O-glycosyl compound
Glycosyl compound
Disaccharide
Methoxyphenol
Benzoate ester
4-alkoxyphenol
Benzoic acid or derivatives
Phenoxy compound
Anisole
Phenol ether
Methoxybenzene
Benzoyl
Phenol
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Oxane
Monocyclic benzene moiety
Benzenoid
Tertiary alcohol
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Ether
Carboxylic acid derivative
Acetal
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	-0.01	ALOGPS
logP	-0.14	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	8.93	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	214.06 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	127.1 m³·mol⁻¹	ChemAxon
Polarizability	53.66 Å³	ChemAxon
Number of Rings	4	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

21615433

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44715598

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Seguinoside E (NP0077740)

MOL for NP0077740 ((-)-Seguinoside E)

3D MOL for NP0077740 ((-)-Seguinoside E)

3D SDF for NP0077740 ((-)-Seguinoside E)

3D-SDF for NP0077740 ((-)-Seguinoside E)

PDB for NP0077740 ((-)-Seguinoside E)

3D PDB for NP0077740 ((-)-Seguinoside E)

SMILES for NP0077740 ((-)-Seguinoside E)

INCHI for NP0077740 ((-)-Seguinoside E)

Structure for NP0077740 ((-)-Seguinoside E)

3D Structure for NP0077740 ((-)-Seguinoside E)