NP-MRD: Showing NP-Card for Benzyl-β-D-glucopyranoside (NP0331190)

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Record Information

Version

2.0

Created at

2022-11-28 18:04:09 UTC

Updated at

2024-09-03 04:21:25 UTC

NP-MRD ID

NP0331190

Natural Product DOI

https://doi.org/10.57994/2484

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Benzyl-β-D-glucopyranoside

Description

ZINC2568371 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. Based on a literature review very few articles have been published on ZINC2568371.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652310172220322D          

 19 20  0  0  1  0            999 V2000
    1.4289   -1.6500    0.0000 O   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 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    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 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  2  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
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  6  0  0  0
  3  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  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
  2 18  1  0  0  0  0
 18 19  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0331190

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@@H]1O[C@H](OCC2=CC=CC=C2)[C@@H](O)[C@H](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-/m0/s1

> <INCHI_KEY>
GKHCBYYBLTXYEV-WJTVCTBASA-N

> <FORMULA>
C13H18O6

> <MOLECULAR_WEIGHT>
270.281

> <EXACT_MASS>
270.1103383

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.582915554618587

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R,5R,6S)-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>
65.28720000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.18e+01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-OCT-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-OCT-22         0                                  
HETATM    1  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.335  -4.620   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  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.000  -9.240   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   18                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    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                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15    2   19                                                  
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₈O₆

Average Mass

270.2810 Da

Monoisotopic Mass

270.11034 Da

IUPAC Name

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

Traditional Name

(2S,3S,4R,5R,6S)-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@H](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-/m0/s1

InChI Key

GKHCBYYBLTXYEV-WJTVCTBASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	hxkuang@hljucm.net	Not Available	Not Available	2024-05-11	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, simulated)	Not Available	Not Available	Not Available	2024-05-11	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Datura metel		Not Available

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	27.58 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

78479810

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

92178844

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Benzyl-β-D-glucopyranoside (NP0331190)

MOL for NP0331190 (Benzyl-β-D-glucopyranoside)

3D MOL for NP0331190 (Benzyl-β-D-glucopyranoside)

3D SDF for NP0331190 (Benzyl-β-D-glucopyranoside)

3D-SDF for NP0331190 (Benzyl-β-D-glucopyranoside)

PDB for NP0331190 (Benzyl-β-D-glucopyranoside)

3D PDB for NP0331190 (Benzyl-β-D-glucopyranoside)

SMILES for NP0331190 (Benzyl-β-D-glucopyranoside)

INCHI for NP0331190 (Benzyl-β-D-glucopyranoside)

Structure for NP0331190 (Benzyl-β-D-glucopyranoside)

3D Structure for NP0331190 (Benzyl-β-D-glucopyranoside)