NP-MRD: Showing NP-Card for (1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid (NP0211408)

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Record Information

Version

2.0

Created at

2022-09-05 09:40:49 UTC

Updated at

2022-09-05 09:40:49 UTC

NP-MRD ID

NP0211408

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid

Description

30046-29-8 Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. (1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid is found in Phaseolus coccineus. Based on a literature review very few articles have been published on 30046-29-8.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052211402D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309052211402D          

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 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 15 14  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  1  0  0  0
 13 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  1  0  0  0
 27 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 11 31  1  6  0  0  0
 32 27  1  1  0  0  0
 11 32  1  0  0  0  0
 32 33  1  0  0  0  0
  4 33  1  0  0  0  0
 33 34  1  6  0  0  0
 34 35  2  0  0  0  0
 34 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0211408

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]12C[C@H](C[C@@]3(OC1=O)[C@@H]1CC[C@]4(O)C[C@]1(CC4=C)[C@H]([C@H]23)C(O)=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O11/c1-10-5-23-9-24(10,33)4-3-13(23)25-7-11(34-20-17(29)16(28)15(27)12(8-26)35-20)6-22(2,21(32)36-25)18(25)14(23)19(30)31/h11-18,20,26-29,33H,1,3-9H2,2H3,(H,30,31)/t11-,12-,13-,14-,15-,16+,17-,18-,20-,22-,23+,24+,25-/m1/s1

> <INCHI_KEY>
LCQKMIMLBQEMSB-VMWKOPFVSA-N

> <FORMULA>
C25H34O11

> <MOLECULAR_WEIGHT>
510.536

> <EXACT_MASS>
510.210111915

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
51.51981811316405

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,5S,8S,9S,10R,11R,13R)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylic acid

> <JCHEM_LOGP>
-1.598517091333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.210573609296567

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9668155617053986

> <JCHEM_PKA_STRONGEST_BASIC>
-0.904636814613394

> <JCHEM_POLAR_SURFACE_AREA>
183.20999999999998

> <JCHEM_REFRACTIVITY>
118.13060000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,5S,8S,9S,10R,11R,13R)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      11.595  -1.236   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.144  -1.999   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.649  -1.346   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.486  -2.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.715  -3.149   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.985  -3.617   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.566  -4.043   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.348  -5.112   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.758  -5.355   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.816  -4.032   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.247  -3.879   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.419  -2.879   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.504  -0.926   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.022  -0.593   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       7.864   1.120   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.466   1.765   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       6.325   3.298   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.926   3.943   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.668   3.054   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       7.582   4.187   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       7.441   5.720   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.981   3.542   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.238   4.431   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       9.122   2.009   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      10.520   1.364   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       5.132  -0.420   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.643  -0.813   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.401   0.243   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.022  -2.221   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       1.385  -2.315   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.735  -3.586   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.829  -2.145   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.217  -1.580   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.138   0.220   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       7.746   0.328   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       4.502   0.889   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10   33                                             
CONECT    5    4    6                                                       
CONECT    6    5    2    7    8                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10   12   31   32                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   26                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15   25                                                  
CONECT   25   24                                                            
CONECT   26   13   27                                                       
CONECT   27   26   28   29   32                                             
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   11                                                       
CONECT   32   27   11   33                                                  
CONECT   33   32    4   34                                                  
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₄O₁₁

Average Mass

510.5360 Da

Monoisotopic Mass

510.21011 Da

IUPAC Name

(1R,2R,5S,8S,9S,10R,11R,13R)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1^{5,8}.0^{1,10}.0^{2,8}]heptadecane-9-carboxylic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@]12C[C@H](C[C@@]3(OC1=O)[C@@H]1CC[C@]4(O)C[C@]1(CC4=C)[C@H]([C@H]23)C(O)=O)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C25H34O11/c1-10-5-23-9-24(10,33)4-3-13(23)25-7-11(34-20-17(29)16(28)15(27)12(8-26)35-20)6-22(2,21(32)36-25)18(25)14(23)19(30)31/h11-18,20,26-29,33H,1,3-9H2,2H3,(H,30,31)/t11-,12-,13-,14-,15-,16+,17-,18-,20-,22-,23+,24+,25-/m1/s1

InChI Key

LCQKMIMLBQEMSB-VMWKOPFVSA-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
Phaseolus coccineus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
20-norgibberellane-6-carboxylic acid
20-norgibberellane diterpenoid
Diterpenoid
Diterpene lactone
Gibberellin
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Caprolactone
Oxepane
Monosaccharide
Gamma butyrolactone
Oxane
Dicarboxylic acid or derivatives
Fatty acyl
Cyclic alcohol
Tetrahydrofuran
Tertiary alcohol
Lactone
Secondary alcohol
Carboxylic acid ester
Polyol
Carboxylic acid derivative
Carboxylic acid
Acetal
Oxacycle
Organoheterocyclic compound
Organooxygen compound
Primary alcohol
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
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	-1.6	ChemAxon
pKa (Strongest Acidic)	3.97	ChemAxon
pKa (Strongest Basic)	-0.9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.21 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	118.13 m³·mol⁻¹	ChemAxon
Polarizability	51.52 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

101288419

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid (NP0211408)

MOL for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

3D MOL for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

3D SDF for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

3D-SDF for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

PDB for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

3D PDB for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

SMILES for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

INCHI for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

Structure for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)

3D Structure for NP0211408 ((1r,2r,5s,8s,9s,10r,11r,13r)-5-hydroxy-11-methyl-6-methylidene-16-oxo-13-{[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-15-oxapentacyclo[9.3.2.1⁵,⁸.0¹,¹⁰.0²,⁸]heptadecane-9-carboxylic acid)