NP-MRD: Showing NP-Card for (1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0209403)

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Record Information

Version

2.0

Created at

2022-09-05 06:48:18 UTC

Updated at

2022-09-05 06:48:18 UTC

NP-MRD ID

NP0209403

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid

Description

(1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D. (1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid is found in Tephroseris rufa. Based on a literature review very few articles have been published on (1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052208482D          

 32 36  0  0  1  0            999 V2000
    0.1083   -0.0934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3468    0.7645    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9499    1.3881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7817    1.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9702    0.3405    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7888    0.1804    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5217    0.9610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3318    0.8015    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1412    0.6418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.5705   -1.1870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5667   -1.5294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0841   -2.1721    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9900   -3.0477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  4  5  1  0  0  0  0
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  7 17  1  0  0  0  0
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  6 20  1  0  0  0  0
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 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 24 31  1  0  0  0  0
 31 32  1  6  0  0  0
M  END

     RDKit          3D

 70 74  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652309052208482D          

 32 36  0  0  1  0            999 V2000
    0.1083   -0.0934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 24 25  1  0  0  0  0
 25 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  1  1  0  0  0
 29 31  1  0  0  0  0
 24 31  1  0  0  0  0
 31 32  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0209403

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]12CCC[C@](C)([C@H]1CC[C@@]13C[C@@H](CC[C@@H]21)C(=C)[C@H]3O[C@@H]1OC[C@H](O)[C@H](O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H38O7/c1-13-14-5-6-17-23(2)8-4-9-24(3,22(29)30)16(23)7-10-25(17,11-14)20(13)32-21-19(28)18(27)15(26)12-31-21/h14-21,26-28H,1,4-12H2,2-3H3,(H,29,30)/t14-,15+,16+,17+,18+,19-,20-,21+,23-,24-,25-/m1/s1

> <INCHI_KEY>
LVDQILCTOJRNNL-HDBBPBHZSA-N

> <FORMULA>
C25H38O7

> <MOLECULAR_WEIGHT>
450.572

> <EXACT_MASS>
450.261753564

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
48.11957638256558

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

> <JCHEM_LOGP>
2.5924264536666684

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.245745198031573

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.473522815535355

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265808814794495

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
115.1759

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-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       0.202  -0.174   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.731   0.014   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.514   1.427   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.640   2.591   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.192   2.219   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.544   0.636   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.072   0.337   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.574   1.794   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.086   1.496   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.597   1.198   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.094  -0.259   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.081  -1.419   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.398  -2.216   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.525  -2.855   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.003  -3.092   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       9.490  -4.055   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       7.570  -1.121   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.564  -2.302   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.035  -2.009   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.401  -0.549   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.521   0.479   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.845  -1.178   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.512  -2.682   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.044  -3.146   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.092  -2.106   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.560  -2.570   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.893  -4.074   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.361  -4.538   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -0.757  -5.114   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.089  -6.617   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.712  -4.649   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       1.848  -5.689   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   20                                                  
CONECT    7    6    8    9   17                                             
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14   17                                             
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   12    7   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19    6   21   22                                             
CONECT   21   20    3                                                       
CONECT   22   20    2   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   31                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   24   32                                                  
CONECT   32   31                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

View in JSmol

Synonyms

Value	Source
(1R,4S,5R,9S,10S,13R,15R)-5,9-Dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0,.0,]hexadecane-5-carboxylate	Generator

Chemical Formula

C₂₅H₃₈O₇

Average Mass

450.5720 Da

Monoisotopic Mass

450.26175 Da

IUPAC Name

(1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

Traditional Name

(1R,4S,5R,9S,10S,13R,15R)-5,9-dimethyl-14-methylidene-15-{[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@@]12CCC[C@](C)([C@H]1CC[C@@]13C[C@@H](CC[C@@H]21)C(=C)[C@H]3O[C@@H]1OC[C@H](O)[C@H](O)[C@H]1O)C(O)=O

InChI Identifier

InChI=1S/C25H38O7/c1-13-14-5-6-17-23(2)8-4-9-24(3,22(29)30)16(23)7-10-25(17,11-14)20(13)32-21-19(28)18(27)15(26)12-31-21/h14-21,26-28H,1,4-12H2,2-3H3,(H,29,30)/t14-,15+,16+,17+,18+,19-,20-,21+,23-,24-,25-/m1/s1

InChI Key

LVDQILCTOJRNNL-HDBBPBHZSA-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
Tephroseris rufa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kaurane diterpenoids. These are diterpene alkaloids with a structure that is based on the kaurane skeleton. Kaurane is a tetracyclic compound that arises by cyclisation of a pimarane precursor followed by rearrangement. It possesses a [3,2,1]-bicyclic ring system with C15-C16 bridge connected to C13, forming the five-membered ring D.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Kaurane diterpenoids

Alternative Parents

Substituents

Kaurane diterpenoid
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Secondary alcohol
Acetal
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Polyol
Organoheterocyclic compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Alcohol
Organic oxygen 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	2.59	ChemAxon
pKa (Strongest Acidic)	4.47	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	115.18 m³·mol⁻¹	ChemAxon
Polarizability	48.12 Å³	ChemAxon
Number of Rings	5	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

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

162977356

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid (NP0209403)

MOL for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D MOL for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D SDF for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D-SDF for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

PDB for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D PDB for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

SMILES for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

INCHI for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

Structure for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)

3D Structure for NP0209403 ((1r,4s,5r,9s,10s,13r,15r)-5,9-dimethyl-14-methylidene-15-{[(2s,3r,4s,5s)-3,4,5-trihydroxyoxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]hexadecane-5-carboxylic acid)