NP-MRD: Showing NP-Card for Neryl glucoside (NP0045343)

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Record Information

Version

2.0

Created at

2022-03-17 19:18:17 UTC

Updated at

2022-03-17 19:18:17 UTC

NP-MRD ID

NP0045343

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Neryl glucoside

Description

Neryl glucoside belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. Neryl glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Neryl glucoside has been detected, but not quantified in, several different foods, such as common grapes, fats and oils, fruits, and tea. This could make neryl glucoside a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 50 50  0  0  0  0  0  0  0  0999 V2000
    6.2160   -0.5935   -1.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7088    0.0276    0.1275 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5730    0.0127    1.3321 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4947    0.5809    0.1222 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6591    0.5840   -1.0784 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4094   -0.2186   -0.8848 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5091    0.2182    0.1637 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8888    0.1851    1.6393 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2829    0.6318   -0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2444    0.6809   -1.4665 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3797   -0.1570   -1.5409 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4152    0.2391   -0.7179 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.6475   -0.7180    0.2121 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8710   -0.9455    0.6864 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8218   -0.7642    2.2150 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0795   -0.9967    2.7118 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0216   -0.1657    0.1933 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.8118   -0.9845   -0.6487 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6914    1.0592   -0.6139 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3065    2.1439    0.1380 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5938    0.6001   -1.5801 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.1034   -0.4864   -2.2815 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2606    0.2046   -1.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4740   -1.3400   -1.4958 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2137   -1.0380   -0.9732 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2405   -0.8230    1.9696 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4052    0.9681    1.8842 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6414   -0.0414    1.0760 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1682    1.0412    1.0299 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3429    1.6484   -1.3068 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2225    0.1995   -1.9658 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9591   -0.5512   -1.8389 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8268   -1.2355   -0.4897 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6730   -0.5235    1.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0382    1.2345    1.9388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9479   -0.1225    2.2055 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3718    0.9566    0.7097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6298    1.7078   -1.7422 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3927    0.3922   -2.2863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1151    1.1655   -0.1933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0929   -2.0503    0.5707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1393   -1.5200    2.6484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4167    0.2268    2.4808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4927   -0.1779    3.0831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7331    0.1215    1.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3862   -0.3834   -1.1928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6069    1.3467   -1.1693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6720    1.9680    0.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2880    1.4379   -2.2261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6164   -1.3355   -2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 14 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 12  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  3 26  1  0
  3 27  1  0
  3 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  6 32  1  0
  6 33  1  0
  8 34  1  0
  8 35  1  0
  8 36  1  0
  9 37  1  0
 10 38  1  0
 10 39  1  0
 12 40  1  1
 14 41  1  1
 15 42  1  0
 15 43  1  0
 16 44  1  0
 17 45  1  1
 18 46  1  0
 19 47  1  6
 20 48  1  0
 21 49  1  6
 22 50  1  0
M  END


  Mrv0541 02241210412D          

 22 22  0  0  0  0            999 V2000
    2.8586    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8586    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1436    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4286    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7150    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0001    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0001    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4287    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4287   -2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1437   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1437   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4287   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4287   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8573   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5723   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0001   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0001   -2.0625    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
  2  4  2  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  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 18  1  0  0  0  0
 12 15  1  0  0  0  0
 13 14  1  0  0  0  0
 13 18  1  0  0  0  0
 14 15  1  0  0  0  0
 14 19  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 22  1  0  0  0  0
 17 18  1  0  0  0  0
 17 21  1  0  0  0  0
 19 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0045343

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C/COC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C16H28O6/c1-10(2)5-4-6-11(3)7-8-21-16-15(20)14(19)13(18)12(9-17)22-16/h5,7,12-20H,4,6,8-9H2,1-3H3/b11-7-

> <INCHI_KEY>
RMMXLHZEVYNSJO-XFFZJAGNSA-N

> <FORMULA>
C16H28O6

> <MOLECULAR_WEIGHT>
316.3899

> <EXACT_MASS>
316.188588628

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
34.80673944872637

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.41

> <JCHEM_LOGP>
0.7315476503333345

> <ALOGPS_LOGS>
-1.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.20007539621729

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210523748540943

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835511357308

> <JCHEM_POLAR_SURFACE_AREA>
99.38000000000001

> <JCHEM_REFRACTIVITY>
83.59539999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.10e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       5.336   5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.336   3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.001   3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   3.850   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.335   3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.000   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.000   5.390   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.332   3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.332   1.540   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.667   0.770   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.667  -5.390   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.002  -1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -4.002  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667  -3.850   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.332  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.332  -1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -5.334  -3.850   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -6.668  -3.080   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -0.000  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -0.000  -3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   18                                                       
CONECT   12   15                                                            
CONECT   13   14   18                                                       
CONECT   14   13   15   19                                                  
CONECT   15   12   14   16                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18   21                                                  
CONECT   18   11   13   17                                                  
CONECT   19   14   20                                                       
CONECT   20   19                                                            
CONECT   21   17                                                            
CONECT   22   16                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Value	Source
1,3-Diaza-spiro[4.6]undecane-2,4-dione	HMDB
1,3-Diazaspiro[4.6]undecane-2,4-dione	HMDB

Chemical Formula

C₁₆H₂₈O₆

Average Mass

316.3899 Da

Monoisotopic Mass

316.18859 Da

IUPAC Name

2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

22850-13-1

SMILES

CC(C)=CCC\C(C)=C/COC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C16H28O6/c1-10(2)5-4-6-11(3)7-8-21-16-15(20)14(19)13(18)12(9-17)22-16/h5,7,12-20H,4,6,8-9H2,1-3H3/b11-7-

InChI Key

RMMXLHZEVYNSJO-XFFZJAGNSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Vitis vinifera L.	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Monoterpenoid
Monocyclic monoterpenoid
Oxane
Monosaccharide
Fatty acyl
Secondary alcohol
Polyol
Acetal
Oxacycle
Organoheterocyclic compound
Primary alcohol
Organooxygen compound
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	0.41	ALOGPS
logP	0.73	ChemAxon
logS	-1.9	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	7	ChemAxon
Refractivity	83.6 m³·mol⁻¹	ChemAxon
Polarizability	34.81 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0029346

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB000413

KNApSAcK ID

Not Available

Chemspider ID

13703052

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

18688993

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Neryl glucoside (NP0045343)

MOL for NP0045343 (Neryl glucoside)

3D MOL for NP0045343 (Neryl glucoside)

3D SDF for NP0045343 (Neryl glucoside)

3D-SDF for NP0045343 (Neryl glucoside)

PDB for NP0045343 (Neryl glucoside)

3D PDB for NP0045343 (Neryl glucoside)

SMILES for NP0045343 (Neryl glucoside)

INCHI for NP0045343 (Neryl glucoside)

Structure for NP0045343 (Neryl glucoside)

3D Structure for NP0045343 (Neryl glucoside)