NP-MRD: Showing NP-Card for 2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0229029)

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Record Information

Version

2.0

Created at

2022-09-06 08:55:10 UTC

Updated at

2022-09-06 08:55:10 UTC

NP-MRD ID

NP0229029

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Description

[6]-Gingerdiol 5-O-beta-D-glucopyranoside belongs to the class of organic compounds known as fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol. [6]-Gingerdiol 5-O-beta-D-glucopyranoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, [6]-Gingerdiol 5-O-beta-D-glucopyranoside has been detected, but not quantified in, herbs and spices. 2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol is found in Zingiber officinale. This could make [6]-gingerdiol 5-O-beta-D-glucopyranoside a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241211322D          

 32 33  0  0  0  0            999 V2000
   -3.6936   -0.2123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6936    0.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287    1.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287    1.9100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4852   -0.6371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0430   -0.6371    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4852    1.0605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501    0.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -0.2123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287   -0.6371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287   -1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2501   -1.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4852   -1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7218   -1.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0430   -1.4853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7217   -1.9100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4852    1.8422    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3119    1.7054    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0430    0.9250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1 10  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  8  2  0  0  0  0
  5 13  1  0  0  0  0
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 23 24  1  0  0  0  0
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 25 30  1  0  0  0  0
 26 27  1  0  0  0  0
 26 31  1  0  0  0  0
 27 32  1  0  0  0  0
 28 29  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv0541 02241211322D          

 32 33  0  0  0  0            999 V2000
   -3.6936   -0.2123    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6936    0.6358    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287    1.0605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9287    1.9100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0229029

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC(CC(O)CCC1=CC(OC)=C(O)C=C1)OC1OC(CO)C(O)C(O)C1O

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

> <INCHI_KEY>
IJSYHUFAWPXPKA-UHFFFAOYSA-N

> <FORMULA>
C23H38O9

> <MOLECULAR_WEIGHT>
458.5424

> <EXACT_MASS>
458.251582814

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
49.910208894069235

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
1.49

> <JCHEM_LOGP>
1.4094818973333332

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.214608154399405

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.27203089827572

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7261417274188977

> <JCHEM_POLAR_SURFACE_AREA>
149.07

> <JCHEM_REFRACTIVITY>
116.66099999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-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      -6.895  -0.396   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.895   1.187   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.467   1.980   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -5.467   3.565   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -2.772  -1.189   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      -0.080  -1.189   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.772   1.980   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.200   1.187   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.200  -0.396   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -5.467  -1.189   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -5.467  -2.773   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.200  -3.565   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.772  -2.773   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.347  -3.565   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.080  -2.773   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.347  -3.565   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.772  -2.773   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.042  -3.565   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.467  -2.773   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.895  -3.565   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.772   3.439   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.184  -0.460   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.449  -1.189   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.711  -0.460   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.711   0.997   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.449   1.724   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.184   0.997   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.976  -1.189   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       6.240  -0.460   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       4.976   1.727   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.449   3.183   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -0.080   1.727   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3                                                            
CONECT    5   13                                                            
CONECT    6   15   22                                                       
CONECT    7    8   21                                                       
CONECT    8    3    7    9                                                  
CONECT    9    8   10                                                       
CONECT   10    1    9   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13    5   12   14                                                  
CONECT   14   13   15                                                       
CONECT   15    6   14   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21    7                                                            
CONECT   22    6   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24   26   30                                                  
CONECT   26   25   27   31                                                  
CONECT   27   22   26   32                                                  
CONECT   28   24   29                                                       
CONECT   29   28                                                            
CONECT   30   25                                                            
CONECT   31   26                                                            
CONECT   32   27                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   66    0
END

View in JSmol

Synonyms

Value	Source
[6]-Gingerdiol 5-O-b-D-glucopyranoside	Generator
[6]-Gingerdiol 5-O-β-D-glucopyranoside	Generator

Chemical Formula

C₂₃H₃₈O₉

Average Mass

458.5424 Da

Monoisotopic Mass

458.25158 Da

IUPAC Name

2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CCCCCC(CC(O)CCC1=CC(OC)=C(O)C=C1)OC1OC(CO)C(O)C(O)C1O

InChI Identifier

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

InChI Key

IJSYHUFAWPXPKA-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 fatty acyl glycosides of mono- and disaccharides. Fatty acyl glycosides of mono- and disaccharides are compounds composed of a mono- or disaccharide moiety linked to one hydroxyl group of a fatty alcohol or of a phosphorylated alcohol (phosphoprenols), a hydroxy fatty acid or to one carboxyl group of a fatty acid (ester linkage) or to an amino alcohol.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl glycosides

Direct Parent

Fatty acyl glycosides of mono- and disaccharides

Alternative Parents

Substituents

Fatty acyl glycoside of mono- or disaccharide
Hexose monosaccharide
Alkyl glycoside
O-glycosyl compound
Glycosyl compound
Methoxyphenol
Fatty alcohol
Methoxybenzene
Phenol ether
Phenoxy compound
Anisole
1-hydroxy-2-unsubstituted benzenoid
Phenol
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Oxane
Monosaccharide
Secondary alcohol
Acetal
Oxacycle
Organoheterocyclic compound
Ether
Polyol
Organic oxygen compound
Hydrocarbon derivative
Primary alcohol
Alcohol
Organooxygen compound
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	1.49	ALOGPS
logP	1.41	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	10.27	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	116.66 m³·mol⁻¹	ChemAxon
Polarizability	49.91 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

HMDB0036123

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014971

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

85163169

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol (NP0229029)

MOL for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0229029 (2-{[3-hydroxy-1-(4-hydroxy-3-methoxyphenyl)decan-5-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol)