NP-MRD: Showing NP-Card for 2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate (NP0289671)

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Record Information

Version

2.0

Created at

2022-09-09 19:58:32 UTC

Updated at

2022-09-09 19:58:33 UTC

NP-MRD ID

NP0289671

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate

Description

2,9-Dihydroxy-2-methyl-8-methylidene-5-(propan-2-yl)cyclodec-3-en-1-yl acetate belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups. 2,9-Dihydroxy-2-methyl-8-methylidene-5-(propan-2-yl)cyclodec-3-en-1-yl acetate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 49 49  0  0  0  0  0  0  0  0999 V2000
    1.0514    2.8691   -0.8619 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2051    2.3649    0.0056 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6811    2.0361    1.3679 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9944    1.2852    1.3525 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414    0.0461    0.4572 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2758   -0.4534    0.2419 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2826   -1.6870   -0.6328 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0644    0.6073   -0.4583 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1469   -0.9756    1.2795 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0401   -1.6160    0.9721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7643   -1.4632   -0.2635 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5605   -2.7558   -0.4816 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0146   -1.2990   -1.4134 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7409   -0.3035   -0.1564 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0812   -0.7480   -0.2580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0037   -0.6602    0.7585 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3773   -1.1586    0.5366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6491   -0.1587    1.8437 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4247    0.8259   -1.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2000    2.1308   -0.3702 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6911    3.1644   -1.1994 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829    3.0520   -0.6150 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7154    3.1122   -1.8572 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0338    1.4924    1.9864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8853    3.0109    1.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8203    1.9319    1.0150 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1633    0.9037    2.3780 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3595    0.3058   -0.4807 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7211   -0.6332    1.2299 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3264   -1.9223   -0.9247 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7178   -1.5455   -1.5563 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9239   -2.5267   -0.0144 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8814    0.0837   -1.0356 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4239    1.1475   -1.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5837    1.3124    0.2043 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6506   -1.1875    2.2434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3196   -2.3414    1.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9344   -3.6441   -0.2549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8596   -2.8562   -1.5480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4404   -2.8077    0.1907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4023   -1.7516   -2.2052 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6344    0.1008    0.8723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1432   -0.4778    1.0025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5748   -1.2123   -0.5356 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5382   -2.1419    1.0532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3594    0.9707   -1.7199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6099    0.5809   -1.8121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8791    2.1275    0.5108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6025    2.8653   -2.1604 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  6  1  0
  6  8  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  2  3
  2 20  1  0
 20 21  1  0
 20 19  1  0
 19 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  2  0
 14 11  1  0
 11 12  1  0
 11 13  1  6
 11 10  1  0
 10  9  2  0
  9  5  1  0
  7 30  1  0
  7 31  1  0
  7 32  1  0
  6 29  1  0
  8 33  1  0
  8 34  1  0
  8 35  1  0
  5 28  1  6
  4 26  1  0
  4 27  1  0
  3 24  1  0
  3 25  1  0
  1 22  1  0
  1 23  1  0
 20 48  1  1
 21 49  1  0
 19 46  1  0
 19 47  1  0
 14 42  1  1
 17 43  1  0
 17 44  1  0
 17 45  1  0
 12 38  1  0
 12 39  1  0
 12 40  1  0
 13 41  1  0
 10 37  1  0
  9 36  1  0
M  END


  Mrv1533004161506222D          

 21 21  0  0  0  0            999 V2000
    3.8068   -0.3883    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2124    0.1837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4105    0.9845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4197   -0.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2216   -0.8460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.0748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8345   -0.5028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0418   -0.7316    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0326    0.2981    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5394    0.9491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4381    0.8701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6363    1.6710    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0418    2.2430    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7508    2.0142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9490    1.2133    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3453    2.5862    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.8998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0660    2.6406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0955    2.3859    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0234    1.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8253    0.5269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 12 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 20 17  1  4  0  0  0
 20 21  2  0  0  0  0
  4 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0289671

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C1CCC(=C)C(O)CC(OC(C)=O)C(C)(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C17H28O4/c1-11(2)14-7-6-12(3)15(19)10-16(21-13(4)18)17(5,20)9-8-14/h8-9,11,14-16,19-20H,3,6-7,10H2,1-2,4-5H3

> <INCHI_KEY>
CQPIRPBIGZJHJS-UHFFFAOYSA-N

> <FORMULA>
C17H28O4

> <MOLECULAR_WEIGHT>
296.407

> <EXACT_MASS>
296.198759382

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
33.20468425964383

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,9-dihydroxy-2-methyl-8-methylidene-5-(propan-2-yl)cyclodec-3-en-1-yl acetate

> <ALOGPS_LOGP>
2.73

> <JCHEM_LOGP>
2.1541274679999987

> <ALOGPS_LOGS>
-2.93

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.60155581852645

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.602466855262968

> <JCHEM_PKA_STRONGEST_BASIC>
-2.999145985872671

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
83.28949999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.52e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  C   UNK     0       7.106  -0.725   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.996   0.343   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.366   1.838   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.517  -0.084   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.147  -1.579   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -2.006   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.558  -0.938   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.078  -1.366   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.928   0.556   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.874   1.772   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.818   1.624   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.188   3.119   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.078   4.187   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      -1.401   3.760   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.771   2.265   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.511   4.828   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.667   3.546   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.990   4.929   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.912   4.454   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.777   2.478   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.407   0.984   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   21                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   12   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17   21                                                       
CONECT   21   20    4                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

View in JSmol

Synonyms

Value	Source
2,9-Dihydroxy-2-methyl-8-methylidene-5-(propan-2-yl)cyclodec-3-en-1-yl acetic acid	Generator

Chemical Formula

C₁₇H₂₈O₄

Average Mass

296.4070 Da

Monoisotopic Mass

296.19876 Da

IUPAC Name

2,9-dihydroxy-2-methyl-8-methylidene-5-(propan-2-yl)cyclodec-3-en-1-yl acetate

Traditional Name

2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate

CAS Registry Number

Not Available

SMILES

CC(C)C1CCC(=C)C(O)CC(OC(C)=O)C(C)(O)C=C1

InChI Identifier

InChI=1S/C17H28O4/c1-11(2)14-7-6-12(3)15(19)10-16(21-13(4)18)17(5,20)9-8-14/h8-9,11,14-16,19-20H,3,6-7,10H2,1-2,4-5H3

InChI Key

CQPIRPBIGZJHJS-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacrane sesquiterpenoids. These are sesquiterpenoids having the germacrane skeleton, with a structure characterized by a cyclodecane ring substituted with an isopropyl and two methyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Germacrane sesquiterpenoids

Alternative Parents

Substituents

Germacrane sesquiterpenoid
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	2.73	ALOGPS
logP	2.15	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	13.6	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	83.29 m³·mol⁻¹	ChemAxon
Polarizability	33.2 Å³	ChemAxon
Number of Rings	1	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

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References

General References

LOTUS database [Link]

Showing NP-Card for 2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate (NP0289671)

MOL for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

3D MOL for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

3D SDF for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

3D-SDF for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

PDB for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

3D PDB for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

SMILES for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

INCHI for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

Structure for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)

3D Structure for NP0289671 (2,9-dihydroxy-5-isopropyl-2-methyl-8-methylidenecyclodec-3-en-1-yl acetate)