NP-MRD: Showing NP-Card for (2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0146412)

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Record Information

Version

2.0

Created at

2022-09-02 01:48:25 UTC

Updated at

2022-09-02 01:48:25 UTC

NP-MRD ID

NP0146412

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Description

Benzyl-beta-d-glucopyranoside 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. (2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol is found in Anethum graveolens, Calanthe discolor, Carum carvi, Coriandrum sativum, Cuminum cyminum, Ficus pumila, Foeniculum vulgare, Glehnia littoralis, Houttuynia cordata, Pimpinella anisum, Prunus armeniaca, Prunus prostrata, Rhodiola sachalinensis, Thunbergia laurifolia and Trachyspermum ammi. Based on a literature review very few articles have been published on benzyl-beta-d-glucopyranoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 38  0  0  0  0  0  0  0  0999 V2000
    2.7155    2.6078   -0.0294 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9513    2.2384    1.0805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4426    0.8223    0.7813 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6922    0.9177   -0.3769 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3393   -0.3248   -0.8947 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5046   -0.0918   -1.9688 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7228   -0.7290   -1.9014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5090   -0.3247   -0.7019 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1695    0.8914   -0.6735 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8905    1.2431    0.4354 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9838    0.4193    1.5392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3231   -0.7800    1.4916 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5933   -1.1478    0.3819 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6552   -0.9415   -1.3916 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4407   -2.0126   -2.2267 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4410   -1.2856   -0.1527 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7260   -2.2363    0.6031 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6286   -0.0647    0.6821 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7684    0.6171    0.1985 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5878    3.5339   -0.2978 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4955    2.2940    2.0223 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0378    2.8831    1.0496 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7888    0.5587    1.6376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0826   -0.9970   -0.1224 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6176   -1.8463   -1.8804 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3104   -0.4001   -2.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0976    1.5364   -1.5352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4077    2.2153    0.4357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5722    0.7471    2.3993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3910   -1.4236    2.3434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1064   -2.1214    0.4383 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1992   -0.1408   -1.9212 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7788   -2.6473   -1.8665 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3995   -1.7022   -0.4594 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7192   -2.0211    1.5543 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8859   -0.4072    1.7198 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5888    0.1202    0.3892 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
  5 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18  3  1  0
 13  8  1  0
  1 20  1  0
  2 21  1  0
  2 22  1  0
  3 23  1  1
  5 24  1  1
  7 25  1  0
  7 26  1  0
  9 27  1  0
 10 28  1  0
 11 29  1  0
 12 30  1  0
 13 31  1  0
 14 32  1  6
 15 33  1  0
 16 34  1  6
 17 35  1  0
 18 36  1  1
 19 37  1  0
M  END


  Mrv1652309022203482D          

 19 20  0  0  1  0            999 V2000
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  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  1  6  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
  3 18  1  0  0  0  0
 18 19  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0146412

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C13H18O6/c14-6-9-10(15)11(16)12(17)13(19-9)18-7-8-4-2-1-3-5-8/h1-5,9-17H,6-7H2/t9-,10+,11?,12-,13-/m1/s1

> <INCHI_KEY>
GKHCBYYBLTXYEV-NRUFJFEESA-N

> <FORMULA>
C13H18O6

> <MOLECULAR_WEIGHT>
270.281

> <EXACT_MASS>
270.1103383

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.353977479764815

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,5R,6R)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.79

> <JCHEM_LOGP>
-0.5649395970000001

> <ALOGPS_LOGS>
-0.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.2000645359077

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210495773683427

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083553633435

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
65.28720000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,5R,6R)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-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       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.669  -7.700   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   18                                                  
CONECT    4    3    5                                                       
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   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16    3   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Value	Source
Benzyl-b-D-glucopyranoside	Generator
Benzyl-β-D-glucopyranoside	Generator

Chemical Formula

C₁₃H₁₈O₆

Average Mass

270.2810 Da

Monoisotopic Mass

270.11034 Da

IUPAC Name

(2R,3R,5R,6R)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

(2R,3R,5R,6R)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C13H18O6/c14-6-9-10(15)11(16)12(17)13(19-9)18-7-8-4-2-1-3-5-8/h1-5,9-17H,6-7H2/t9-,10+,11?,12-,13-/m1/s1

InChI Key

GKHCBYYBLTXYEV-NRUFJFEESA-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
Anethum graveolens	LOTUS Database	35616633
Calanthe discolor	LOTUS Database	35616633
Carum carvi	LOTUS Database	35616633
Coriandrum sativum	LOTUS Database	35616633
Cuminum cyminum	LOTUS Database	35616633
Ficus pumila	LOTUS Database	35616633
Foeniculum vulgare	LOTUS Database	35616633
Glehnia littoralis	LOTUS Database	35616633
Houttuynia cordata	LOTUS Database	35616633
Pimpinella anisum	LOTUS Database	35616633
Prunus armeniaca	LOTUS Database	35616633
Prunus prostrata	LOTUS Database	35616633
Rhodiola sachalinensis	LOTUS Database	35616633
Thunbergia laurifolia	LOTUS Database	35616633
Trachyspermum ammi	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

Hexose monosaccharide
O-glycosyl compound
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Primary alcohol
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	-0.79	ALOGPS
logP	-0.56	ChemAxon
logS	-0.93	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	99.38 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	65.29 m³·mol⁻¹	ChemAxon
Polarizability	27.35 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

67168181

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13254166

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0146412)

MOL for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0146412 ((2r,3r,5r,6r)-2-(benzyloxy)-6-(hydroxymethyl)oxane-3,4,5-triol)