NP-MRD: Showing NP-Card for Panaxydol (NP0137004)

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Record Information

Version

2.0

Created at

2022-05-30 16:38:43 UTC

Updated at

2022-05-30 16:38:43 UTC

NP-MRD ID

NP0137004

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Panaxydol

Description

Panaxydol belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms. Thus, panaxydol is considered to be a fatty alcohol lipid molecule. Panaxydol is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Outside of the human body, Panaxydol has been detected, but not quantified in, tea. Panaxydol is found in Niphogeton ternata, Panax ginseng, Panax notoginseng, Panax pseudoginseng and Panax quinquefolius. This could make panaxydol a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 43  0  0  0  0  0  0  0  0999 V2000
    7.1365    1.7976    1.6823 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4913    2.4246    0.5730 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8834    2.1348   -0.7315 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.8351    1.4155   -1.4823 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6689    1.3150   -0.5223 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6885    0.6348   -0.3399 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5464   -0.1804   -0.1098 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5883   -0.8896    0.0872 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4416   -1.7699    0.3293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694   -1.7187   -0.8219 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3443   -2.8158   -1.6644 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7349   -2.5443   -0.7359 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9484   -2.0789   -1.4745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1107   -1.7786   -0.5628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7858   -0.6957    0.4392 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9859   -0.4604    1.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2015   -0.0267    0.5568 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0173    1.2651   -0.1994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6587    2.3692    0.7944 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5714    1.9997    2.6370 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3658    1.0399    1.6223 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2627    3.1802    0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6342    3.0926   -1.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5020    0.4855   -1.5456 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8068   -2.8231    0.5026 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9295   -1.4049    1.2476 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3826   -0.7448   -1.3316 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8223   -3.3808   -0.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2342   -2.8339   -2.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7232   -1.1495   -2.0296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4064   -2.7211   -0.0739 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9768   -1.4266   -1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9556   -1.0174    1.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4053    0.2203   -0.0565 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2221   -1.4120    1.8145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7242    0.3507    2.0194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6161   -0.8021   -0.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0022    0.1664    1.3148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9817    1.5729   -0.6520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2634    1.2309   -0.9791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0121    2.0718    1.8076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1824    3.3267    0.5217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5779    2.5808    0.8015 H   0  0  0  0  0  0  0  0  0  0  0  0
 19 18  1  0
 18 17  1  0
 17 16  1  0
 16 15  1  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  3  0
  7  6  1  0
  6  5  3  0
  5  3  1  0
  3  4  1  0
  3  2  1  0
  2  1  2  3
 10 12  1  0
 19 41  1  0
 19 42  1  0
 19 43  1  0
 18 39  1  0
 18 40  1  0
 17 37  1  0
 17 38  1  0
 16 35  1  0
 16 36  1  0
 15 33  1  0
 15 34  1  0
 14 31  1  0
 14 32  1  0
 13 29  1  0
 13 30  1  0
 12 28  1  1
 10 27  1  6
  9 25  1  0
  9 26  1  0
  3 23  1  6
  4 24  1  0
  2 22  1  0
  1 20  1  0
  1 21  1  0
M  END

  Mrv0541 05061307292D          

 19 19  0  0  0  0            999 V2000
   -4.3164   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2256   -0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6020   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5112   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8875   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1730   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4586   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6533   -1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3677   -0.9059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7441   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9388   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0822   -0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0296   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2243   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7967   -0.0809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6849   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5099   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7967    0.7441    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0974   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  3  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  1  0  0  0  0
  9  8  1  0  0  0  0
 10  7  1  0  0  0  0
 11  8  3  0  0  0  0
 12  9  3  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15  4  1  0  0  0  0
 15 12  1  0  0  0  0
 16 13  1  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 18 15  1  0  0  0  0
 19 16  1  0  0  0  0
 19 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137004

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCC1OC1CC#CC#CC(O)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C17H24O2/c1-3-5-6-7-10-13-16-17(19-16)14-11-8-9-12-15(18)4-2/h4,15-18H,2-3,5-7,10,13-14H2,1H3

> <INCHI_KEY>
GVLDSGIQZAFIAN-UHFFFAOYSA-N

> <FORMULA>
C17H24O2

> <MOLECULAR_WEIGHT>
260.3713

> <EXACT_MASS>
260.177630012

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
32.898713508739846

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
8-(3-heptyloxiran-2-yl)oct-1-en-4,6-diyn-3-ol

> <ALOGPS_LOGP>
4.68

> <JCHEM_LOGP>
4.5119963819999995

> <ALOGPS_LOGS>
-4.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.668319073133024

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.293537750389156

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5452057555158127

> <JCHEM_POLAR_SURFACE_AREA>
32.76

> <JCHEM_REFRACTIVITY>
79.66849999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.48e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
panaxydol

> <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      -8.057  -4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.488  -0.151   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.724  -3.231   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.154  -0.921   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.390  -4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.056  -3.231   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.723  -4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.819  -2.461   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.153  -1.691   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.389  -3.231   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.486  -3.231   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.487  -0.921   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.055  -4.001   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.152  -4.001   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.821  -0.151   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.278  -3.231   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.818  -3.231   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.821   1.389   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       2.048  -1.897   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    4                                                            
CONECT    3    1    5                                                       
CONECT    4    2   15                                                       
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6   10                                                       
CONECT    8    9   11                                                       
CONECT    9    8   12                                                       
CONECT   10    7   13                                                       
CONECT   11    8   14                                                       
CONECT   12    9   15                                                       
CONECT   13   10   16                                                       
CONECT   14   11   17                                                       
CONECT   15    4   12   18                                                  
CONECT   16   13   17   19                                                  
CONECT   17   14   16   19                                                  
CONECT   18   15                                                            
CONECT   19   16   17                                                       
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

View in JSmol

Synonyms

Value	Source
(-)-Panaxydol	HMDB
8-(3-Heptyloxiranyl)-1-octene-4,6-diyn-3-ol	HMDB
8-(3-Heptyloxiranyl)-1-octene-4,6-diyn-3-ol, 9ci	HMDB
9,10-Epoxy-1-heptadecene-4,6-diyn-3-ol	HMDB

Chemical Formula

C₁₇H₂₄O₂

Average Mass

260.3713 Da

Monoisotopic Mass

260.17763 Da

IUPAC Name

8-(3-heptyloxiran-2-yl)oct-1-en-4,6-diyn-3-ol

Traditional Name

panaxydol

CAS Registry Number

Not Available

SMILES

CCCCCCCC1OC1CC#CC#CC(O)C=C

InChI Identifier

InChI=1S/C17H24O2/c1-3-5-6-7-10-13-16-17(19-16)14-11-8-9-12-15(18)4-2/h4,15-18H,2-3,5-7,10,13-14H2,1H3

InChI Key

GVLDSGIQZAFIAN-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
Niphogeton ternata	LOTUS Database	35616633
Panax ginseng	LOTUS Database	35616633
Panax notoginseng	LOTUS Database	35616633
Panax pseudoginseng	LOTUS Database	35616633
Panax quinquefolius	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty alcohols. These are aliphatic alcohols consisting of a chain of a least six carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Fatty alcohols

Alternative Parents

Substituents

Fatty alcohol
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Ether
Oxirane
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Fatty alcohols (LMFA05000028 )

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	4.68	ALOGPS
logP	4.51	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	13.29	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.76 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	79.67 m³·mol⁻¹	ChemAxon
Polarizability	32.9 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

HMDB0034000

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB012234

KNApSAcK ID

C00030922

Chemspider ID

4446401

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5283280

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Panaxydol (NP0137004)

MOL for NP0137004 (Panaxydol)

3D MOL for NP0137004 (Panaxydol)

3D SDF for NP0137004 (Panaxydol)

3D-SDF for NP0137004 (Panaxydol)

PDB for NP0137004 (Panaxydol)

3D PDB for NP0137004 (Panaxydol)

SMILES for NP0137004 (Panaxydol)

INCHI for NP0137004 (Panaxydol)

Structure for NP0137004 (Panaxydol)

3D Structure for NP0137004 (Panaxydol)