NP-MRD: Showing NP-Card for (2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate (NP0181582)

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Record Information

Version

2.0

Created at

2022-09-03 20:07:36 UTC

Updated at

2022-09-03 20:07:36 UTC

NP-MRD ID

NP0181582

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate

Description

Pseudopterosin R belongs to the class of organic compounds known as amphilectane, neoamphilectane, cycloamphilectane, and adociane diterpenoids. These are diterpenoids with a structure based on the amphilectane or a seco-,neo-, or cyclo- derivative thereof. Amphilectane is a tricyclic structure made up of three cyclohexane fused together, with a methyl group at the C11-, C7-, and C3- positions. Additionally, it carries a 2-methylpropyl group at the C1-position. Amphilectanes are presumably derived from serrulatanes. Cycloamphilectanes represent a further cyclisation. (2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate is found in Antillogorgia elisabethae. Based on a literature review very few articles have been published on Pseudopterosin R.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032222072D          

 35 38  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309032222072D          

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  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  5  4  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 10 16  1  0  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 22 21  1  6  0  0  0
 14 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 13 26  1  0  0  0  0
 26 27  1  1  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
  8 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
  5 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0181582

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@@H](C=C(C)C)C2=C3[C@@H]1CC[C@H](C)C3=C(O)C(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](OC(C)=O)[C@@H]1O)=C2C

> <INCHI_IDENTIFIER>
InChI=1S/C28H40O7/c1-12(2)10-18-11-14(4)19-9-8-13(3)20-22(19)21(18)15(5)26(24(20)31)35-28-25(32)27(34-17(7)29)23(30)16(6)33-28/h10,13-14,16,18-19,23,25,27-28,30-32H,8-9,11H2,1-7H3/t13-,14-,16-,18+,19+,23+,25-,27+,28-/m0/s1

> <INCHI_KEY>
REFOFWBTJBXTFK-CKELVKOMSA-N

> <FORMULA>
C28H40O7

> <MOLECULAR_WEIGHT>
488.621

> <EXACT_MASS>
488.277403628

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
54.90389481238084

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R,5R,6S)-2-{[(1S,3S,7S,9aR)-6-hydroxy-1,4,7-trimethyl-3-(2-methylprop-1-en-1-yl)-2,3,7,8,9,9a-hexahydro-1H-phenalen-5-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate

> <JCHEM_LOGP>
4.964675533666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.265058254595013

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.452012285824832

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6269858274845843

> <JCHEM_POLAR_SURFACE_AREA>
105.45000000000002

> <JCHEM_REFRACTIVITY>
132.9304

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R,5R,6S)-2-{[(4S,6S,6aR,9S)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4H-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0     -10.669  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -9.336  -0.770   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -8.002   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   34                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   31                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   26                                                  
CONECT   14   13   15   22                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   10   17                                                  
CONECT   17   16                                                            
CONECT   18   15   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   14   23                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   13   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31    8   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    5   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₀O₇

Average Mass

488.6210 Da

Monoisotopic Mass

488.27740 Da

IUPAC Name

(2S,3S,4R,5R,6S)-2-{[(1S,3S,7S,9aR)-6-hydroxy-1,4,7-trimethyl-3-(2-methylprop-1-en-1-yl)-2,3,7,8,9,9a-hexahydro-1H-phenalen-5-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate

Traditional Name

(2S,3S,4R,5R,6S)-2-{[(4S,6S,6aR,9S)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4H-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@@H](C=C(C)C)C2=C3[C@@H]1CC[C@H](C)C3=C(O)C(O[C@@H]1O[C@@H](C)[C@@H](O)[C@@H](OC(C)=O)[C@@H]1O)=C2C

InChI Identifier

InChI=1S/C28H40O7/c1-12(2)10-18-11-14(4)19-9-8-13(3)20-22(19)21(18)15(5)26(24(20)31)35-28-25(32)27(34-17(7)29)23(30)16(6)33-28/h10,13-14,16,18-19,23,25,27-28,30-32H,8-9,11H2,1-7H3/t13-,14-,16-,18+,19+,23+,25-,27+,28-/m0/s1

InChI Key

REFOFWBTJBXTFK-CKELVKOMSA-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
Antillogorgia elisabethae	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as amphilectane, neoamphilectane, cycloamphilectane, and adociane diterpenoids. These are diterpenoids with a structure based on the amphilectane or a seco-,neo-, or cyclo- derivative thereof. Amphilectane is a tricyclic structure made up of three cyclohexane fused together, with a methyl group at the C11-, C7-, and C3- positions. Additionally, it carries a 2-methylpropyl group at the C1-position. Amphilectanes are presumably derived from serrulatanes. Cycloamphilectanes represent a further cyclisation.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Amphilectane, neoamphilectane, cycloamphilectane, and adociane diterpenoids

Alternative Parents

Substituents

Amphilectane, neoamphilectane, cycloamphilectane, or adociane diterpenoid
Fatty acyl glycoside
Phenolic glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Tetralin
Fatty acyl
Monosaccharide
Oxane
Benzenoid
Carboxylic acid ester
Secondary alcohol
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Acetal
Oxacycle
Carboxylic acid derivative
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	4.96	ChemAxon
pKa (Strongest Acidic)	10.45	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	105.45 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	132.93 m³·mol⁻¹	ChemAxon
Polarizability	54.9 Å³	ChemAxon
Number of Rings	4	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

9652167

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11477339

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate (NP0181582)

MOL for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

3D MOL for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

3D SDF for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

3D-SDF for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

PDB for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

3D PDB for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

SMILES for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

INCHI for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

Structure for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)

3D Structure for NP0181582 ((2s,3s,4r,5r,6s)-2-{[(4s,6s,6ar,9s)-1-hydroxy-3,6,9-trimethyl-4-(2-methylprop-1-en-1-yl)-5,6,6a,7,8,9-hexahydro-4h-phenalen-2-yl]oxy}-3,5-dihydroxy-6-methyloxan-4-yl acetate)