NP-MRD: Showing NP-Card for β-d-glucopyranoside, phenyl (NP0171861)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-03 08:33:24 UTC

Updated at

2022-09-03 08:33:24 UTC

NP-MRD ID

NP0171861

Secondary Accession Numbers

None

Natural Product Identification

Common Name

β-d-glucopyranoside, phenyl

Description

PHENYLALPHA-D-GLUCOPYRANOSIDE 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. β-d-glucopyranoside, phenyl is found in Gymnadenia conopsea. PHENYLALPHA-D-GLUCOPYRANOSIDE is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
   -2.8142    2.4056   -1.9672 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4402    2.4836   -0.6497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8940    1.1813   -0.1094 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7744    0.7830   -0.8223 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0423   -0.1325   -0.0268 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1534   -0.4235   -0.6704 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4336   -0.2991   -0.2223 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4918   -0.6443   -1.0204 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8058   -0.5298   -0.5949 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0586   -0.0539    0.6707 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9946    0.2927    1.4719 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6789    0.1738    1.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8799   -1.4084   -0.0422 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2799   -2.3282    0.8349 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2848   -1.1794    0.3896 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4469   -1.2195    1.7760 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9008    0.0774   -0.1281 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.0052    0.3736    0.6857 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5125    3.0253   -2.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6282    3.2370   -0.5606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2989    2.7742    0.0004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5685    1.3419    0.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0625    0.2580    1.0026 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3703   -1.0287   -2.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6406   -0.8057   -1.2340 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0899    0.0312    0.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2291    0.6630    2.4606 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9216    0.4758    1.7493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8414   -1.8261   -1.0555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8139   -3.1381    0.9282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9031   -2.0388   -0.0027 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9701   -1.9832    2.1935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2609   -0.0796   -1.1703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3708   -0.4586    1.1192 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  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
  5 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 15 17  1  0
 17 18  1  0
 17  3  1  0
 12  7  1  0
  1 19  1  0
  2 20  1  0
  2 21  1  0
  3 22  1  1
  5 23  1  1
  8 24  1  0
  9 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  6
 14 30  1  0
 15 31  1  6
 16 32  1  0
 17 33  1  6
 18 34  1  0
M  END


  Mrv1533004201503122D          

 18 19  0  0  0  0            999 V2000
    1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    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
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    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
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
  7 12  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  1  0  0  0  0
  3 17  1  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0171861

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1OC(OC2=CC=CC=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C12H16O6/c13-6-8-9(14)10(15)11(16)12(18-8)17-7-4-2-1-3-5-7/h1-5,8-16H,6H2

> <INCHI_KEY>
NEZJDVYDSZTRFS-UHFFFAOYSA-N

> <FORMULA>
C12H16O6

> <MOLECULAR_WEIGHT>
256.254

> <EXACT_MASS>
256.094688235

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
24.958597399155497

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(hydroxymethyl)-6-phenoxyoxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.64

> <JCHEM_LOGP>
-0.5983875990000002

> <ALOGPS_LOGS>
-0.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.196091454684598

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.200141777338832

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981092343686484

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
60.183299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.72e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-D-glucopyranoside, phenyl

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  O   UNK     0       2.667   0.000   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.668  -5.390   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       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    7                                                       
CONECT   13    5   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    3   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   38    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₁₆O₆

Average Mass

256.2540 Da

Monoisotopic Mass

256.09469 Da

IUPAC Name

2-(hydroxymethyl)-6-phenoxyoxane-3,4,5-triol

Traditional Name

β-D-glucopyranoside, phenyl

CAS Registry Number

Not Available

SMILES

OCC1OC(OC2=CC=CC=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C12H16O6/c13-6-8-9(14)10(15)11(16)12(18-8)17-7-4-2-1-3-5-7/h1-5,8-16H,6H2

InChI Key

NEZJDVYDSZTRFS-UHFFFAOYSA-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
Gymnadenia conopsea	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
O-glycosyl compound
Phenoxy compound
Phenol ether
Monocyclic benzene moiety
Monosaccharide
Benzenoid
Oxane
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Polyol
Alcohol
Primary alcohol
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD0-1668 )

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	-0.64	ALOGPS
logP	-0.6	ChemAxon
logS	-0.73	ALOGPS
pKa (Strongest Acidic)	12.2	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	3	ChemAxon
Refractivity	60.18 m³·mol⁻¹	ChemAxon
Polarizability	24.96 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

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

313297

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for β-d-glucopyranoside, phenyl (NP0171861)

MOL for NP0171861 (β-d-glucopyranoside, phenyl)

3D MOL for NP0171861 (β-d-glucopyranoside, phenyl)

3D SDF for NP0171861 (β-d-glucopyranoside, phenyl)

3D-SDF for NP0171861 (β-d-glucopyranoside, phenyl)

PDB for NP0171861 (β-d-glucopyranoside, phenyl)

3D PDB for NP0171861 (β-d-glucopyranoside, phenyl)

SMILES for NP0171861 (β-d-glucopyranoside, phenyl)

INCHI for NP0171861 (β-d-glucopyranoside, phenyl)

Structure for NP0171861 (β-d-glucopyranoside, phenyl)

3D Structure for NP0171861 (β-d-glucopyranoside, phenyl)