NP-MRD: Showing NP-Card for [(3s,4s,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 furan-2-carboxylate (NP0290413)

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Record Information

Version

2.0

Created at

2022-09-09 21:05:16 UTC

Updated at

2022-09-09 21:05:16 UTC

NP-MRD ID

NP0290413

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3s,4s,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 furan-2-carboxylate

Description

[(3S,4S,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 furan-2-carboxylate 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,4s,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 furan-2-carboxylate is found in Myrsine seguinii. Based on a literature review very few articles have been published on [(3S,4S,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 furan-2-carboxylate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092223052D          

 35 38  0  0  1  0            999 V2000
    2.1102   -0.5392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3033   -0.3677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7512   -0.9808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0557   -0.8092    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6078   -1.4223    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1598   -0.8092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0597   -1.9072    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1953   -2.6919    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0203   -2.6919    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5052   -3.3593    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1696   -4.1130    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309092223052D          

 35 38  0  0  1  0            999 V2000
    2.1102   -0.5392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3033   -0.3677    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0290413

> <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=CO3)[C@@H]2O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C22H26O13/c23-8-14-15(25)16(26)17(20(34-14)33-12-5-3-11(24)4-6-12)35-21-18(27)22(29,10-32-21)9-31-19(28)13-2-1-7-30-13/h1-7,14-18,20-21,23-27,29H,8-10H2/t14-,15-,16+,17-,18-,20-,21+,22-/m1/s1

> <INCHI_KEY>
OOMRRHXBUCKSRD-YSVABYHYSA-N

> <FORMULA>
C22H26O13

> <MOLECULAR_WEIGHT>
498.437

> <EXACT_MASS>
498.137340897

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
47.5767630470839

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3S,4S,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 furan-2-carboxylate

> <JCHEM_LOGP>
-0.6229054879999996

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.796943302012847

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.817606235032184

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810925692673598

> <JCHEM_POLAR_SURFACE_AREA>
197.74

> <JCHEM_REFRACTIVITY>
111.04730000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4S,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 furan-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  O   UNK     0       3.939  -1.006   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.433  -0.686   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.402  -1.831   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.104  -1.511   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.134  -2.655   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.165  -1.511   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.111  -3.560   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.364  -5.025   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.904  -5.025   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.810  -6.271   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.183  -7.678   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.652  -7.839   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.253  -6.593   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       1.785  -6.754   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.690  -5.508   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.222  -5.669   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.848  -7.076   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.380  -7.237   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       3.943  -8.321   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.411  -8.160   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -0.025  -9.245   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -0.931 -10.491   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.304 -11.898   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.209 -13.144   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.462 -10.330   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.367 -11.576   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -3.088  -8.923   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -4.620  -8.762   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.380  -3.560   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.845  -3.084   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.957   0.778   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       0.492   1.254   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       0.492   2.794   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.957   3.270   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.862   2.024   0.000  0.00  0.00           O+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   35                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   31                                                       
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
[(3S,4S,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 furan-2-carboxylic acid	Generator

Chemical Formula

C₂₂H₂₆O₁₃

Average Mass

498.4370 Da

Monoisotopic Mass

498.13734 Da

IUPAC Name

[(3S,4S,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 furan-2-carboxylate

Traditional Name

[(3S,4S,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 furan-2-carboxylate

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=CO3)[C@@H]2O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C22H26O13/c23-8-14-15(25)16(26)17(20(34-14)33-12-5-3-11(24)4-6-12)35-21-18(27)22(29,10-32-21)9-31-19(28)13-2-1-7-30-13/h1-7,14-18,20-21,23-27,29H,8-10H2/t14-,15-,16+,17-,18-,20-,21+,22-/m1/s1

InChI Key

OOMRRHXBUCKSRD-YSVABYHYSA-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
Furoic acid ester
4-alkoxyphenol
Furoic acid or derivatives
Phenoxy compound
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Oxane
Tertiary alcohol
Tetrahydrofuran
Furan
Heteroaromatic compound
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Acetal
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Alcohol
Primary 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	-0.62	ChemAxon
pKa (Strongest Acidic)	9.82	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	197.74 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	111.05 m³·mol⁻¹	ChemAxon
Polarizability	47.58 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

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

162914824

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(3s,4s,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 furan-2-carboxylate (NP0290413)

MOL for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

3D MOL for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

3D SDF for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

3D-SDF for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

PDB for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

3D PDB for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

SMILES for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

INCHI for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

Structure for NP0290413 ([(3s,4s,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 furan-2-carboxylate)

3D Structure for NP0290413 ([(3s,4s,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 furan-2-carboxylate)