NP-MRD: Showing NP-Card for 5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol (NP0185249)

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Record Information

Version

2.0

Created at

2022-09-04 00:36:08 UTC

Updated at

2022-09-04 00:36:09 UTC

NP-MRD ID

NP0185249

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol

Description

5'-(Hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosane-6,2'-piperidin]-18-ene-10,16-diol belongs to the class of organic compounds known as spirosolanes and derivatives. These are steroidal alkaloids with a structure containing a spirosolane skeleton. Siporosolane is a polycyclic compound that is characterized by a 1-oxa-6-azaspiro[4.5]Decane moiety where the oxolane ring is fused to a docosahydronaphth[2,1:4',5']Indene ring system. Spirosolane arises from the conversion of a cholestane side-chain into a bicyclic system containing a piperidine and a tetrahydrofuran ring. 5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol is found in Solanum nigrum. 5'-(Hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]Icosane-6,2'-piperidin]-18-ene-10,16-diol is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171520352D          

 32 37  0  0  0  0            999 V2000
    7.2076   -4.2801    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3319   -3.4645    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0648   -3.0857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9311   -2.2716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6640   -1.8929    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2507   -2.4728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0743   -2.4249    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4446   -1.6877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2682   -1.6397    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7215   -2.3290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.9984   -2.9704    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8221   -2.9224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6282   -3.7076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.8046   -3.7555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3512   -3.0662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9810   -3.8035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.2223   -2.2464    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
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  3 22  1  0  0  0  0
  6 22  1  0  0  0  0
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 29 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  0  0  0  0
 25 32  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1533004171520352D          

 32 37  0  0  0  0            999 V2000
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 15 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
  7 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
  3 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  1  0  0  0  0
  4 24  1  0  0  0  0
 24 25  1  0  0  0  0
  2 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  0  0  0  0
 25 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0185249

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1C2C(CC3C4CC=C5CC(O)CCC5(C)C4CC(O)C23C)OC11CCC(CO)CN1

> <INCHI_IDENTIFIER>
InChI=1S/C27H43NO4/c1-15-24-22(32-27(15)9-6-16(14-29)13-28-27)11-21-19-5-4-17-10-18(30)7-8-25(17,2)20(19)12-23(31)26(21,24)3/h4,15-16,18-24,28-31H,5-14H2,1-3H3

> <INCHI_KEY>
RFENQHCDYDELRG-UHFFFAOYSA-N

> <FORMULA>
C27H43NO4

> <MOLECULAR_WEIGHT>
445.644

> <EXACT_MASS>
445.319208869

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
53.08867011387156

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol

> <ALOGPS_LOGP>
2.65

> <JCHEM_LOGP>
1.983944590666665

> <ALOGPS_LOGS>
-4.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.50221249464953

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.607727245364671

> <JCHEM_PKA_STRONGEST_BASIC>
9.077677564950381

> <JCHEM_POLAR_SURFACE_AREA>
81.95

> <JCHEM_REFRACTIVITY>
125.29219999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.35e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      13.454  -7.989   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.686  -6.467   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.054  -5.760   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.805  -4.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.173  -3.533   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.268  -4.616   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.805  -4.526   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      19.497  -3.150   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      21.034  -3.061   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      21.880  -4.347   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      23.418  -4.258   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.264  -5.545   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      25.801  -5.455   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      23.573  -6.921   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.035  -7.010   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      21.189  -5.724   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      20.498  -7.100   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      19.652  -5.813   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      18.960  -7.189   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      17.423  -7.279   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.732  -8.655   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      16.577  -5.992   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      15.746  -7.289   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      13.282  -4.008   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      12.591  -5.384   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      12.048  -6.825   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.528  -7.075   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.552  -5.884   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.032  -6.134   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       7.489  -7.574   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.095  -4.443   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      11.615  -4.193   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
CONECT    3    2    4   22                                                  
CONECT    4    3    5   24                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   22                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10   17   18                                             
CONECT   17   16                                                            
CONECT   18   16    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20    3    6   23                                             
CONECT   23   22                                                            
CONECT   24    4   25                                                       
CONECT   25   24    2   26   32                                             
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32                                                       
CONECT   32   31   25                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₃NO₄

Average Mass

445.6440 Da

Monoisotopic Mass

445.31921 Da

IUPAC Name

5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol

Traditional Name

5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol

CAS Registry Number

Not Available

SMILES

CC1C2C(CC3C4CC=C5CC(O)CCC5(C)C4CC(O)C23C)OC11CCC(CO)CN1

InChI Identifier

InChI=1S/C27H43NO4/c1-15-24-22(32-27(15)9-6-16(14-29)13-28-27)11-21-19-5-4-17-10-18(30)7-8-25(17,2)20(19)12-23(31)26(21,24)3/h4,15-16,18-24,28-31H,5-14H2,1-3H3

InChI Key

RFENQHCDYDELRG-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
Solanum nigrum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as spirosolanes and derivatives. These are steroidal alkaloids with a structure containing a spirosolane skeleton. Siporosolane is a polycyclic compound that is characterized by a 1-oxa-6-azaspiro[4.5]Decane moiety where the oxolane ring is fused to a docosahydronaphth[2,1:4',5']Indene ring system. Spirosolane arises from the conversion of a cholestane side-chain into a bicyclic system containing a piperidine and a tetrahydrofuran ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Spirosolanes and derivatives

Alternative Parents

Substituents

Spirosolane skeleton
3-hydroxy-delta-5-steroid
3-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
Azasteroid
Delta-5-steroid
Azaspirodecane
Alkaloid or derivatives
Piperidine
Cyclic alcohol
Tetrahydrofuran
Hemiaminal
Secondary alcohol
Oxacycle
Azacycle
Secondary aliphatic amine
Organoheterocyclic compound
Secondary amine
Alcohol
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Amine
Primary alcohol
Organonitrogen compound
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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	2.65	ALOGPS
logP	1.98	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	14.61	ChemAxon
pKa (Strongest Basic)	9.08	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	81.95 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	125.29 m³·mol⁻¹	ChemAxon
Polarizability	53.09 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

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

73796889

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol (NP0185249)

MOL for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

3D MOL for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

3D SDF for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

3D-SDF for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

PDB for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

3D PDB for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

SMILES for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

INCHI for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

Structure for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)

3D Structure for NP0185249 (5'-(hydroxymethyl)-7,9,13-trimethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidin]-18-ene-10,16-diol)