NP-MRD: Showing NP-Card for (1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate (NP0253865)

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Record Information

Version

2.0

Created at

2022-09-07 17:51:39 UTC

Updated at

2022-09-07 17:51:39 UTC

NP-MRD ID

NP0253865

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate

Description

Harpagoside B belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton. (1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate is found in Scrophularia deserti. (1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate was first documented in 2017 (PMID: 28496487). Based on a literature review a small amount of articles have been published on Harpagoside B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072219512D          

 36 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072219512D          

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 19 20  1  6  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  1  1  0  0  0
 26 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 21 30  1  0  0  0  0
 30 31  1  1  0  0  0
 19 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
  3 35  1  0  0  0  0
 18 35  1  0  0  0  0
 35 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0253865

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@@H]1C[C@](C)(OC(=O)\C=C\C2=CC=CC=C2)[C@@H]2[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)OC=C[C@@]12O

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O11/c1-24(36-17(27)9-8-14-6-4-3-5-7-14)12-16(32-2)25(31)10-11-33-23(21(24)25)35-22-20(30)19(29)18(28)15(13-26)34-22/h3-11,15-16,18-23,26,28-31H,12-13H2,1-2H3/b9-8+/t15-,16-,18-,19+,20-,21+,22+,23+,24+,25-/m1/s1

> <INCHI_KEY>
BEHDYQAAWZWDFR-VWMBWHKBSA-N

> <FORMULA>
C25H32O11

> <MOLECULAR_WEIGHT>
508.52

> <EXACT_MASS>
508.19446185

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
51.00306741457429

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4aS,5R,7S,7aR)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-7-yl (2E)-3-phenylprop-2-enoate

> <JCHEM_LOGP>
-0.3137971833333328

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.801786148521558

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.126316963852394

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981084760235162

> <JCHEM_POLAR_SURFACE_AREA>
164.37

> <JCHEM_REFRACTIVITY>
123.52280000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4aS,5R,7S,7aR)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,5H,6H,7aH-cyclopenta[c]pyran-7-yl (2E)-3-phenylprop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       2.680  -5.158   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.792   0.713   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.752   1.350   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.847   2.596   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.315   2.435   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.473   4.003   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.568   5.249   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.194   6.655   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.289   7.901   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.916   9.308   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.447   9.469   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.352   8.223   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.726   6.816   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       6.258   2.547   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.258   4.087   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       7.591   4.857   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.591   6.397   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       6.258   7.167   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       8.925   4.087   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      10.259   4.857   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.925   2.547   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      10.259   1.777   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       7.591   1.777   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.591   0.237   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       6.258  -0.533   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       3.429  -3.604   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   35                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7   18                                             
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12                                                       
CONECT   18    5   19   35                                                  
CONECT   19   18   20   32                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   30                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   21   31                                                  
CONECT   31   30                                                            
CONECT   32   19   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34    3   18   36                                             
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₂O₁₁

Average Mass

508.5200 Da

Monoisotopic Mass

508.19446 Da

IUPAC Name

(1S,4aS,5R,7S,7aR)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,4aH,5H,6H,7H,7aH-cyclopenta[c]pyran-7-yl (2E)-3-phenylprop-2-enoate

Traditional Name

(1S,4aS,5R,7S,7aR)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1H,5H,6H,7aH-cyclopenta[c]pyran-7-yl (2E)-3-phenylprop-2-enoate

CAS Registry Number

Not Available

SMILES

CO[C@@H]1C[C@](C)(OC(=O)\C=C\C2=CC=CC=C2)[C@@H]2[C@H](O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)OC=C[C@@]12O

InChI Identifier

InChI=1S/C25H32O11/c1-24(36-17(27)9-8-14-6-4-3-5-7-14)12-16(32-2)25(31)10-11-33-23(21(24)25)35-22-20(30)19(29)18(28)15(13-26)34-22/h3-11,15-16,18-23,26,28-31H,12-13H2,1-2H3/b9-8+/t15-,16-,18-,19+,20-,21+,22+,23+,24+,25-/m1/s1

InChI Key

BEHDYQAAWZWDFR-VWMBWHKBSA-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
Scrophularia deserti	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoid o-glycosides. These are iridoid monoterpenes containing a glycosyl (usually a pyranosyl) moiety linked to the iridoid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Iridoid O-glycosides

Alternative Parents

Substituents

Iridoid o-glycoside
Cinnamic acid or derivatives
Hexose monosaccharide
Cinnamic acid ester
O-glycosyl compound
Iridoid-skeleton
Glycosyl compound
Aromatic monoterpenoid
Monoterpenoid
Bicyclic monoterpenoid
Styrene
Fatty acid ester
Monosaccharide
Fatty acyl
Monocyclic benzene moiety
Benzenoid
Oxane
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Cyclic alcohol
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Polyol
Ether
Dialkyl ether
Acetal
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Alcohol
Primary alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen 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	-0.31	ChemAxon
pKa (Strongest Acidic)	12.13	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	164.37 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	123.52 m³·mol⁻¹	ChemAxon
Polarizability	51 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00039336

Chemspider ID

5293892

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6918699

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pasdaran A, Delazar A, Ayatollahi SA, Pasdaran A: Chemical Composition and Biological Activities of Methanolic Extract of Scrophularia Oxysepala Boiss. Iran J Pharm Res. 2017 Winter;16(1):338-346. [PubMed:28496487 ]
LOTUS database [Link]

Showing NP-Card for (1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate (NP0253865)

MOL for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

3D MOL for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

3D SDF for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

3D-SDF for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

PDB for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

3D PDB for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

SMILES for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

INCHI for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

Structure for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)

3D Structure for NP0253865 ((1s,4as,5r,7s,7ar)-4a-hydroxy-5-methoxy-7-methyl-1-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1h,5h,6h,7ah-cyclopenta[c]pyran-7-yl (2e)-3-phenylprop-2-enoate)