NP-MRD: Showing NP-Card for (3s,10s)-panaxydiol (NP0294532)

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Record Information

Version

2.0

Created at

2022-09-10 03:07:21 UTC

Updated at

2022-09-10 03:07:22 UTC

NP-MRD ID

NP0294532

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,10s)-panaxydiol

Description

1,8-Heptadecadiene-4,6-diyne-3,10-diol, also known as 1,8-HDDDD, belongs to the class of organic compounds known as long-chain fatty alcohols. These are fatty alcohols that have an aliphatic tail of 13 to 21 carbon atoms. (3s,10s)-panaxydiol is found in Panax ginseng and Panax japonicus. Based on a literature review very few articles have been published on 1,8-Heptadecadiene-4,6-diyne-3,10-diol.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 42  0  0  0  0  0  0  0  0999 V2000
   -8.1718   -0.8439   -0.7218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3490    0.3486   -0.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6226    0.7535    1.0030 C   0  0  2  0  0  0  0  0  0  0  0  0
   -7.6534    2.1540    1.1211 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2328    0.3100    0.8840 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0812   -0.0522    0.8062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7201   -0.4757    0.7388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5693   -0.8336    0.7029 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1978   -1.2575    0.6849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5883   -1.6627   -0.4070 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8296   -2.0871   -0.3561 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0005   -3.1343   -1.2601 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6825   -0.9336   -0.8391 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5867    0.2631    0.0525 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4553    1.3613   -0.4906 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8984    0.9965   -0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5051    0.6308    0.7453 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9612    0.2742    0.5725 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7732    1.4135   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4861   -1.5335   -0.2583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7097   -1.1325   -1.6075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0391    1.0320   -0.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0956    0.3681    1.9338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7780    2.4520    1.4639 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6019   -1.2550    1.6103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1268   -1.6850   -1.3431 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1253   -2.3889    0.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8992   -3.5531   -1.1618 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7365   -1.3077   -0.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3688   -0.6587   -1.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5241    0.6207    0.0009 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7819    0.0310    1.0980 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3777    2.2737    0.1709 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1152    1.7071   -1.4860 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0799    0.1699   -1.2905 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4506    1.8841   -0.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0086   -0.2154    1.2207 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4194    1.5087    1.4331 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3774    0.0697    1.5845 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0455   -0.6279   -0.0365 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7101    1.3453   -1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8444    1.2817    0.2486 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4667    2.3886    0.3896 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 11  1  0
 11 12  1  0
 11 10  1  0
 10  9  2  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
 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
 11 27  1  1
 12 28  1  0
 10 26  1  0
  9 25  1  0
  3 23  1  1
  4 24  1  0
  2 22  1  0
  1 20  1  0
  1 21  1  0
M  END


  Mrv1652309102205072D          

 19 18  0  0  1  0            999 V2000
   -1.2888    6.6809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5743    6.2684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5743    5.4434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.2888    5.0309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401    5.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    4.6184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5691    4.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    3.7934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    3.3809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  3  0  0  0  0
  6  7  1  0  0  0  0
  7  8  3  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  1  6  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0294532

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCC[C@H](O)\C=C\C#CC#C[C@@H](O)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C17H24O2/c1-3-5-6-7-11-14-17(19)15-12-9-8-10-13-16(18)4-2/h4,12,15-19H,2-3,5-7,11,14H2,1H3/b15-12+/t16-,17-/m0/s1

> <INCHI_KEY>
DSVMWGREWREVQQ-LHGWUTHLSA-N

> <FORMULA>
C17H24O2

> <MOLECULAR_WEIGHT>
260.377

> <EXACT_MASS>
260.177630013

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
32.98011509910363

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,8E,10S)-heptadeca-1,8-dien-4,6-diyne-3,10-diol

> <JCHEM_LOGP>
4.2191822199999995

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.20915661299667

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.185129431662986

> <JCHEM_PKA_STRONGEST_BASIC>
-1.832514897475257

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
82.7797

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,8E,10S)-heptadeca-1,8-dien-4,6-diyne-3,10-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.406  12.471   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.072  11.701   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.072  10.161   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.406   9.391   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.262   9.391   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.595   8.621   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.929   7.851   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.263   7.081   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.596   6.311   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      16.266   4.771   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Value	Source
1,8-HDDDD	MeSH

Chemical Formula

C₁₇H₂₄O₂

Average Mass

260.3770 Da

Monoisotopic Mass

260.17763 Da

IUPAC Name

(3S,8E,10S)-heptadeca-1,8-dien-4,6-diyne-3,10-diol

Traditional Name

(3S,8E,10S)-heptadeca-1,8-dien-4,6-diyne-3,10-diol

CAS Registry Number

Not Available

SMILES

CCCCCCC[C@H](O)\C=C\C#CC#C[C@@H](O)C=C

InChI Identifier

InChI=1S/C17H24O2/c1-3-5-6-7-11-14-17(19)15-12-9-8-10-13-16(18)4-2/h4,12,15-19H,2-3,5-7,11,14H2,1H3/b15-12+/t16-,17-/m0/s1

InChI Key

DSVMWGREWREVQQ-LHGWUTHLSA-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
Panax ginseng	LOTUS Database	35616633
Panax Japonicus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as long-chain fatty alcohols. These are fatty alcohols that have an aliphatic tail of 13 to 21 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty alcohols

Direct Parent

Long-chain fatty alcohols

Alternative Parents

Substituents

Long chain fatty alcohol
Secondary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

long-chain fatty alcohol (CHEBI:67997 )

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	4.22	ChemAxon
pKa (Strongest Acidic)	13.19	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	40.46 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	82.78 m³·mol⁻¹	ChemAxon
Polarizability	32.98 Å³	ChemAxon
Number of Rings	0	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00031489

Chemspider ID

8643212

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10467801

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s,10s)-panaxydiol (NP0294532)

MOL for NP0294532 ((3s,10s)-panaxydiol)

3D MOL for NP0294532 ((3s,10s)-panaxydiol)

3D SDF for NP0294532 ((3s,10s)-panaxydiol)

3D-SDF for NP0294532 ((3s,10s)-panaxydiol)

PDB for NP0294532 ((3s,10s)-panaxydiol)

3D PDB for NP0294532 ((3s,10s)-panaxydiol)

SMILES for NP0294532 ((3s,10s)-panaxydiol)

INCHI for NP0294532 ((3s,10s)-panaxydiol)

Structure for NP0294532 ((3s,10s)-panaxydiol)

3D Structure for NP0294532 ((3s,10s)-panaxydiol)