NP-MRD: Showing NP-Card for 2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol (NP0190952)

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Record Information

Version

2.0

Created at

2022-09-04 07:43:50 UTC

Updated at

2022-09-04 07:43:50 UTC

NP-MRD ID

NP0190952

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Description

[6]-Gingerdiol 4'-O-beta-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. [6]-Gingerdiol 4'-O-beta-D-glucopyranoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, [6]-Gingerdiol 4'-O-beta-D-glucopyranoside has been detected, but not quantified in, herbs and spices. 2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol is found in Zingiber officinale. This could make [6]-gingerdiol 4'-O-beta-D-glucopyranoside a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061308532D          

 32 33  0  0  0  0            999 V2000
    5.7158    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8618    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1473    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5762    7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8618    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    9.4875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    8.6625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749    6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  9  7  1  0  0  0  0
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 31 17  1  0  0  0  0
 31 23  1  0  0  0  0
 32 19  1  0  0  0  0
 32 23  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv0541 05061308532D          

 32 33  0  0  0  0            999 V2000
    5.7158    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   17.1473    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4328    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    8.2500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184    7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5762    7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0190952

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC(O)CC(O)CCC1=CC(OC)=C(OC2OC(CO)C(O)C(O)C2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C23H38O9/c1-3-4-5-6-15(25)12-16(26)9-7-14-8-10-17(18(11-14)30-2)31-23-22(29)21(28)20(27)19(13-24)32-23/h8,10-11,15-16,19-29H,3-7,9,12-13H2,1-2H3

> <INCHI_KEY>
NIZBVVCYJIIIMW-UHFFFAOYSA-N

> <FORMULA>
C23H38O9

> <MOLECULAR_WEIGHT>
458.5424

> <EXACT_MASS>
458.251582814

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
49.992092213452636

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
1.18

> <JCHEM_LOGP>
0.9122494496666667

> <ALOGPS_LOGS>
-2.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.187889483064883

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.199090419450592

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7208398973095154

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
116.39209999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      10.669  15.400   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      26.674  10.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.003  16.170   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.337  15.400   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.671  16.170   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.004  15.400   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.673  16.170   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.340  16.170   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.339  15.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      26.674  15.400   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      24.006  13.860   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      18.672  15.400   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      33.342  13.090   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      24.006  15.400   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      17.338  16.170   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      20.005  16.170   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      26.674  13.860   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      25.340  13.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      32.008  13.860   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      32.008  15.400   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      30.675  16.170   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      29.341  15.400   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      29.341  13.860   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      34.676  13.860   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      17.338  17.710   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      20.005  17.710   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      33.342  16.170   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      30.675  17.710   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      28.007  16.170   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      25.340  11.550   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      28.007  13.090   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      30.675  13.090   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2   30                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5   15                                                       
CONECT    7    9   14                                                       
CONECT    8   10   14                                                       
CONECT    9    7   16                                                       
CONECT   10    8   17                                                       
CONECT   11   14   18                                                       
CONECT   12   15   16                                                       
CONECT   13   19   24                                                       
CONECT   14    7    8   11                                                  
CONECT   15    6   12   25                                                  
CONECT   16    9   12   26                                                  
CONECT   17   10   18   31                                                  
CONECT   18   11   17   30                                                  
CONECT   19   13   20   32                                                  
CONECT   20   19   21   27                                                  
CONECT   21   20   22   28                                                  
CONECT   22   21   23   29                                                  
CONECT   23   22   31   32                                                  
CONECT   24   13                                                            
CONECT   25   15                                                            
CONECT   26   16                                                            
CONECT   27   20                                                            
CONECT   28   21                                                            
CONECT   29   22                                                            
CONECT   30    2   18                                                       
CONECT   31   17   23                                                       
CONECT   32   19   23                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
[6]-Gingerdiol 4'-O-b-D-glucopyranoside	Generator
[6]-Gingerdiol 4'-O-β-D-glucopyranoside	Generator

Chemical Formula

C₂₃H₃₈O₉

Average Mass

458.5424 Da

Monoisotopic Mass

458.25158 Da

IUPAC Name

2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CCCCCC(O)CC(O)CCC1=CC(OC)=C(OC2OC(CO)C(O)C(O)C2O)C=C1

InChI Identifier

InChI=1S/C23H38O9/c1-3-4-5-6-15(25)12-16(26)9-7-14-8-10-17(18(11-14)30-2)31-23-22(29)21(28)20(27)19(13-24)32-23/h8,10-11,15-16,19-29H,3-7,9,12-13H2,1-2H3

InChI Key

NIZBVVCYJIIIMW-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
Zingiber officinale	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
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
O-glycosyl compound
Fatty alcohol
Phenoxy compound
Methoxybenzene
Anisole
Phenol ether
Alkyl aryl ether
Fatty acyl
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Secondary alcohol
Organoheterocyclic compound
Ether
Oxacycle
Polyol
Acetal
Hydrocarbon derivative
Alcohol
Primary 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	1.18	ALOGPS
logP	0.91	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	149.07 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	116.39 m³·mol⁻¹	ChemAxon
Polarizability	49.99 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0036122

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014970

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

85182103

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol (NP0190952)

MOL for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0190952 (2-[4-(3,5-dihydroxydecyl)-2-methoxyphenoxy]-6-(hydroxymethyl)oxane-3,4,5-triol)