NP-MRD: Showing NP-Card for [(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-hydroxybenzoate (NP0230169)

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Record Information

Version

2.0

Created at

2022-09-06 10:32:21 UTC

Updated at

2022-09-06 10:32:21 UTC

NP-MRD ID

NP0230169

Secondary Accession Numbers

None

Natural Product Identification

Common 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-hydroxybenzoate

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-hydroxybenzoate belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. [(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-hydroxybenzoate 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-hydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062212322D          

 37 40  0  0  1  0            999 V2000
    1.0722   -0.7325    0.0000 O   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


  Mrv1652309062212322D          

 37 40  0  0  1  0            999 V2000
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 21 22  1  0  0  0  0
 22 23  1  6  0  0  0
 23 24  1  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  0  0  0  0
 11 27  1  0  0  0  0
 27 28  1  6  0  0  0
  9 29  1  0  0  0  0
  5 29  1  0  0  0  0
 29 30  1  6  0  0  0
  2 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
 34 36  1  0  0  0  0
 36 37  2  0  0  0  0
 31 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0230169

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC=C(O)C=C2)[C@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=C(O)C=C3)[C@H]2O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O13/c25-9-16-17(28)18(29)19(22(36-16)35-15-7-5-14(27)6-8-15)37-23-20(30)24(32,11-34-23)10-33-21(31)12-1-3-13(26)4-2-12/h1-8,16-20,22-23,25-30,32H,9-11H2/t16-,17-,18+,19-,20+,22-,23+,24-/m1/s1

> <INCHI_KEY>
GDCHGVOUTCXBSI-JALRXJJFSA-N

> <FORMULA>
C24H28O13

> <MOLECULAR_WEIGHT>
524.475

> <EXACT_MASS>
524.152990962

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
50.6466933871646

> <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-hydroxybenzoate

> <JCHEM_LOGP>
0.013282546333334398

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.837687211774186

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.477172816918033

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810925692673598

> <JCHEM_POLAR_SURFACE_AREA>
204.82999999999998

> <JCHEM_REFRACTIVITY>
120.63729999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <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-hydroxybenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       2.001  -1.367   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.495  -1.047   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.535  -2.192   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.042  -1.871   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.072  -3.016   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.103  -1.871   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.826  -3.921   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.302  -5.386   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -3.842  -5.386   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -4.747  -6.632   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.121  -8.038   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.589  -8.199   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.684  -6.954   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -0.153  -7.115   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.753  -5.869   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.284  -6.030   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.910  -7.436   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.442  -7.597   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.005  -8.682   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.474  -8.521   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -1.963  -9.606   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.868 -10.852   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.242 -12.259   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -3.147 -13.505   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -4.400 -10.691   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -5.305 -11.937   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -5.026  -9.284   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.558  -9.123   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -4.318  -3.921   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -5.783  -3.445   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.019   0.417   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.487   0.738   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.963   2.202   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.933   3.347   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.408   4.811   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       0.574   3.027   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.050   1.562   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7   29                                             
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   29                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   27                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   14                                                       
CONECT   21   12   22                                                       
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23                                                            
CONECT   25   22   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   11   28                                                  
CONECT   28   27                                                            
CONECT   29    9    5   30                                                  
CONECT   30   29                                                            
CONECT   31    2   32   37                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   31                                                       
MASTER        0    0    0    0    0    0    0    0   37    0   80    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-hydroxybenzoic acid	Generator

Chemical Formula

C₂₄H₂₈O₁₃

Average Mass

524.4750 Da

Monoisotopic Mass

524.15299 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-hydroxybenzoate

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-hydroxybenzoate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC=C(O)C=C2)[C@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=C(O)C=C3)[C@H]2O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C24H28O13/c25-9-16-17(28)18(29)19(22(36-16)35-15-7-5-14(27)6-8-15)37-23-20(30)24(32,11-34-23)10-33-21(31)12-1-3-13(26)4-2-12/h1-8,16-20,22-23,25-30,32H,9-11H2/t16-,17-,18+,19-,20+,22-,23+,24-/m1/s1

InChI Key

GDCHGVOUTCXBSI-JALRXJJFSA-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
Myrsine seguinii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
Disaccharide
O-glycosyl compound
P-hydroxybenzoic acid ester
P-hydroxybenzoic acid alkyl ester
Benzoate ester
4-alkoxyphenol
Benzoic acid or derivatives
Phenoxy compound
Phenol ether
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Oxane
Tetrahydrofuran
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Acetal
Organic oxide
Primary alcohol
Hydrocarbon derivative
Alcohol
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	0.013	ChemAxon
pKa (Strongest Acidic)	8.48	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	204.83 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	120.64 m³·mol⁻¹	ChemAxon
Polarizability	50.65 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

21615432

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45359609

PDB ID

Not Available

ChEBI ID

184006

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(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-hydroxybenzoate (NP0230169)

MOL for NP0230169 ([(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-hydroxybenzoate)

3D MOL for NP0230169 ([(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-hydroxybenzoate)

3D SDF for NP0230169 ([(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-hydroxybenzoate)

3D-SDF for NP0230169 ([(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-hydroxybenzoate)

PDB for NP0230169 ([(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-hydroxybenzoate)

3D PDB for NP0230169 ([(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-hydroxybenzoate)

SMILES for NP0230169 ([(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-hydroxybenzoate)

INCHI for NP0230169 ([(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-hydroxybenzoate)

Structure for NP0230169 ([(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-hydroxybenzoate)

3D Structure for NP0230169 ([(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-hydroxybenzoate)