NP-MRD: Showing NP-Card for [(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate (NP0271286)

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Record Information

Version

2.0

Created at

2022-09-08 17:31:57 UTC

Updated at

2022-09-08 17:31:57 UTC

NP-MRD ID

NP0271286

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate

Description

[(3S,4R,5S)-5-{[(2R,3R,4S,5R,6R)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. [(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate is found in Viscum articulatum. Based on a literature review very few articles have been published on [(3S,4R,5S)-5-{[(2R,3R,4S,5R,6R)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082219312D          

 36 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309082219312D          

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 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
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0271286

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OCC2=CC=CC=C2)[C@H](O)[C@@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=CC=C3)[C@H]2O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O11/c26-11-17-18(27)20(19(28)23(35-17)32-12-15-7-3-1-4-8-15)36-24-21(29)25(31,14-34-24)13-33-22(30)16-9-5-2-6-10-16/h1-10,17-21,23-24,26-29,31H,11-14H2/t17-,18-,19-,20+,21+,23-,24+,25-/m1/s1

> <INCHI_KEY>
JIJCXJQRKVPZKK-YADPSDQBSA-N

> <FORMULA>
C25H30O11

> <MOLECULAR_WEIGHT>
506.504

> <EXACT_MASS>
506.178811786

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
51.15634273917455

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
0.6538611916666663

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.350097919028155

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.711011701732247

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810907776490874

> <JCHEM_POLAR_SURFACE_AREA>
164.37

> <JCHEM_REFRACTIVITY>
121.77940000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-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      -1.963  -9.606   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.431  -9.767   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.195 -11.174   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -2.868 -10.852   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -4.400 -10.691   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -5.305 -11.937   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -4.679 -13.344   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -5.584 -14.590   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.957 -15.997   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -5.863 -17.243   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -7.394 -17.082   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.021 -15.675   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -7.115 -14.429   0.000  0.00  0.00           C+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  C   UNK     0       0.574   3.027   0.000  0.00  0.00           C+0
HETATM   36  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   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21                                                       
CONECT   27   18   11   28                                                  
CONECT   28   27                                                            
CONECT   29    9    5   30                                                  
CONECT   30   29                                                            
CONECT   31    2   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

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

Chemical Formula

C₂₅H₃₀O₁₁

Average Mass

506.5040 Da

Monoisotopic Mass

506.17881 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OCC2=CC=CC=C2)[C@H](O)[C@@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=CC=C3)[C@H]2O)[C@@H]1O

InChI Identifier

InChI=1S/C25H30O11/c26-11-17-18(27)20(19(28)23(35-17)32-12-15-7-3-1-4-8-15)36-24-21(29)25(31,14-34-24)13-33-22(30)16-9-5-2-6-10-16/h1-10,17-21,23-24,26-29,31H,11-14H2/t17-,18-,19-,20+,21+,23-,24+,25-/m1/s1

InChI Key

JIJCXJQRKVPZKK-YADPSDQBSA-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
Viscum articulatum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Disaccharide
O-glycosyl compound
Benzoate ester
Benzoic acid or derivatives
Benzoyl
Benzenoid
Oxane
Monocyclic benzene moiety
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Primary alcohol
Organic oxide
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	0.65	ChemAxon
pKa (Strongest Acidic)	11.71	ChemAxon
pKa (Strongest Basic)	-3	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	10	ChemAxon
Refractivity	121.78 m³·mol⁻¹	ChemAxon
Polarizability	51.16 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

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

163011615

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate (NP0271286)

MOL for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D MOL for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D SDF for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D-SDF for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

PDB for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D PDB for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

SMILES for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

INCHI for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

Structure for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)

3D Structure for NP0271286 ([(3s,4r,5s)-5-{[(2r,3r,4s,5r,6r)-2-(benzyloxy)-3,5-dihydroxy-6-(hydroxymethyl)oxan-4-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl benzoate)