NP-MRD: Showing NP-Card for aphanalide I (NP0043482)

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Record Information

Version

1.0

Created at

2021-06-21 00:52:53 UTC

Updated at

2021-06-30 00:19:11 UTC

NP-MRD ID

NP0043482

Secondary Accession Numbers

None

Natural Product Identification

Common Name

aphanalide I

Provided By

JEOL Database JEOL Logo

Description

CHEMBL2392326 belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17. aphanalide I is found in Aphanamixis grandifolia. It was first documented in 2002 (PMID: 29437326). Based on a literature review a significant number of articles have been published on CHEMBL2392326 (PMID: 27466641) (PMID: 27253005) (PMID: 26389468) (PMID: 26389426).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306212102523D          

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M  END


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M  END
> <DATABASE_ID>
NP0043482

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])[C@]([H])(O[H])[C@@]2(C([H])([H])[H])[C@]([H])(C3=C([H])OC([H])=C3[H])C([H])([H])C(=O)[C@@]2([H])[C@]2(C([H])([H])[H])[C@]([H])(O[H])C([H])([H])[C@]3([H])[C@@](C([H])=C([H])C(=O)OC3(C([H])([H])[H])C([H])([H])[H])(C([H])([H])[H])[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C26H34O7/c1-23(2)16-11-17(28)26(5)20-15(27)10-14(13-7-9-32-12-13)25(20,4)22(31)19(30)21(26)24(16,3)8-6-18(29)33-23/h6-9,12,14,16-17,19-22,28,30-31H,10-11H2,1-5H3/t14-,16-,17+,19+,20+,21+,22-,24-,25-,26-/m0/s1

> <INCHI_KEY>
ZKJDMXKOBXJDDB-MGJCYGGASA-N

> <FORMULA>
C26H34O7

> <MOLECULAR_WEIGHT>
458.551

> <EXACT_MASS>
458.230453435

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
48.532857047083446

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2R,8R,10R,11R,12S,15R,16S,17R,18R)-15-(furan-3-yl)-10,17,18-trihydroxy-2,7,7,11,16-pentamethyl-6-oxatetracyclo[9.7.0.0^{2,8}.0^{12,16}]octadec-3-ene-5,13-dione

> <ALOGPS_LOGP>
2.68

> <JCHEM_LOGP>
1.678118471666667

> <ALOGPS_LOGS>
-3.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.50165779455023

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.463876311213099

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8775210914813623

> <JCHEM_POLAR_SURFACE_AREA>
117.20000000000002

> <JCHEM_REFRACTIVITY>
120.03849999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.03e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,8R,10R,11R,12S,15R,16S,17R,18R)-15-(furan-3-yl)-10,17,18-trihydroxy-2,7,7,11,16-pentamethyl-6-oxatetracyclo[9.7.0.0^{2,8}.0^{12,16}]octadec-3-ene-5,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 16 51  1  0
 16 52  1  0
M  END

HEADER    PROTEIN                                 21-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JUN-21         0                                  
HETATM    1  C   UNK     0      -3.418  -3.677   2.974  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.166  -3.752   2.067  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.419  -4.903   1.073  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.052  -4.202   2.860  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.658  -3.375   3.848  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.023  -3.437   5.010  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.449  -2.532   3.392  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.578  -2.012   2.162  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.384  -2.017   0.956  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.145  -3.073  -0.034  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.878  -2.352   1.395  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.888  -2.090   0.257  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.858  -0.663  -0.273  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.359   0.182   0.762  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.451  -0.188  -0.749  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.176  -0.879  -2.105  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.448   1.380  -0.863  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.460   1.966  -1.836  0.00  0.00           C+0
HETATM   19  O   UNK     0      -3.667   1.769  -1.761  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.834   2.876  -2.852  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.373   2.438  -2.780  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.581   3.399  -3.419  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.644   4.818  -3.297  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.693   5.238  -4.079  0.00  0.00           C+0
HETATM   25  O   UNK     0       2.278   4.178  -4.688  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.597   3.074  -4.300  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.114   2.071  -1.281  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.077   3.322  -0.385  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.090   1.122  -1.151  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.337   1.828  -1.027  0.00  0.00           O+0
HETATM   31  C   UNK     0       1.020   0.148   0.046  0.00  0.00           C+0
HETATM   32  O   UNK     0       2.079  -0.789  -0.161  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.371  -0.528   0.349  0.00  0.00           C+0
HETATM   34  H   UNK     0      -4.339  -3.542   2.398  0.00  0.00           H+0
HETATM   35  H   UNK     0      -3.521  -4.592   3.569  0.00  0.00           H+0
HETATM   36  H   UNK     0      -3.348  -2.849   3.688  0.00  0.00           H+0
HETATM   37  H   UNK     0      -2.548  -5.849   1.613  0.00  0.00           H+0
HETATM   38  H   UNK     0      -3.318  -4.747   0.470  0.00  0.00           H+0
HETATM   39  H   UNK     0      -1.574  -5.065   0.402  0.00  0.00           H+0
HETATM   40  H   UNK     0       1.214  -2.366   4.143  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.524  -1.497   2.006  0.00  0.00           H+0
HETATM   42  H   UNK     0       1.056  -2.770  -0.553  0.00  0.00           H+0
HETATM   43  H   UNK     0       0.394  -4.009   0.480  0.00  0.00           H+0
HETATM   44  H   UNK     0      -0.581  -3.322  -0.810  0.00  0.00           H+0
HETATM   45  H   UNK     0      -2.103  -1.609   2.177  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.903  -2.278   0.628  0.00  0.00           H+0
HETATM   47  H   UNK     0      -2.731  -2.790  -0.568  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.574  -0.616  -1.103  0.00  0.00           H+0
HETATM   49  H   UNK     0      -3.939   0.838   0.323  0.00  0.00           H+0
HETATM   50  H   UNK     0      -0.120  -0.919  -2.370  0.00  0.00           H+0
HETATM   51  H   UNK     0      -1.710  -0.379  -2.920  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.523  -1.914  -2.125  0.00  0.00           H+0
HETATM   53  H   UNK     0      -1.730   1.791   0.116  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.994   3.914  -2.548  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.261   2.704  -3.844  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.308   1.509  -3.367  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.008   5.464  -2.706  0.00  0.00           H+0
HETATM   58  H   UNK     0       2.126   6.204  -4.300  0.00  0.00           H+0
HETATM   59  H   UNK     0       1.949   2.143  -4.725  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.183   3.031   0.667  0.00  0.00           H+0
HETATM   61  H   UNK     0       0.971   3.895  -0.648  0.00  0.00           H+0
HETATM   62  H   UNK     0      -0.778   4.003  -0.447  0.00  0.00           H+0
HETATM   63  H   UNK     0       1.221   0.538  -2.066  0.00  0.00           H+0
HETATM   64  H   UNK     0       2.433   2.427  -1.790  0.00  0.00           H+0
HETATM   65  H   UNK     0       1.309   0.701   0.950  0.00  0.00           H+0
HETATM   66  H   UNK     0       2.877  -0.244  -0.322  0.00  0.00           H+0
HETATM   67  H   UNK     0      -0.717   0.071   1.211  0.00  0.00           H+0
CONECT    1    2   34   35   36                                             
CONECT    2   11    4    1    3                                             
CONECT    3    2   37   38   39                                             
CONECT    4    5    2                                                       
CONECT    5    6    4    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   40                                                  
CONECT    8    9    7   41                                                  
CONECT    9    8   10   11   33                                             
CONECT   10    9   42   43   44                                             
CONECT   11   12    2   45    9                                             
CONECT   12   11   13   46   47                                             
CONECT   13   12   15   14   48                                             
CONECT   14   13   49                                                       
CONECT   15   13   33   17   16                                             
CONECT   16   15   50   51   52                                             
CONECT   17   53   15   27   18                                             
CONECT   18   20   19   17                                                  
CONECT   19   18                                                            
CONECT   20   18   21   54   55                                             
CONECT   21   20   27   22   56                                             
CONECT   22   21   26   23                                                  
CONECT   23   24   22   57                                                  
CONECT   24   25   23   58                                                  
CONECT   25   26   24                                                       
CONECT   26   22   25   59                                                  
CONECT   27   21   28   29   17                                             
CONECT   28   27   60   61   62                                             
CONECT   29   30   27   31   63                                             
CONECT   30   29   64                                                       
CONECT   31   33   32   29   65                                             
CONECT   32   31   66                                                       
CONECT   33   15   31   67    9                                             
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    1                                                            
CONECT   37    3                                                            
CONECT   38    3                                                            
CONECT   39    3                                                            
CONECT   40    7                                                            
CONECT   41    8                                                            
CONECT   42   10                                                            
CONECT   43   10                                                            
CONECT   44   10                                                            
CONECT   45   11                                                            
CONECT   46   12                                                            
CONECT   47   12                                                            
CONECT   48   13                                                            
CONECT   49   14                                                            
CONECT   50   16                                                            
CONECT   51   16                                                            
CONECT   52   16                                                            
CONECT   53   17                                                            
CONECT   54   20                                                            
CONECT   55   20                                                            
CONECT   56   21                                                            
CONECT   57   23                                                            
CONECT   58   24                                                            
CONECT   59   26                                                            
CONECT   60   28                                                            
CONECT   61   28                                                            
CONECT   62   28                                                            
CONECT   63   29                                                            
CONECT   64   30                                                            
CONECT   65   31                                                            
CONECT   66   32                                                            
CONECT   67   33                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  142    0
END

RDKit          3D

67 71  0  0  0  0  0  0  0  0999 V2000
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 16 52  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₄O₇

Average Mass

458.5510 Da

Monoisotopic Mass

458.23045 Da

IUPAC Name

(1R,2R,8R,10R,11R,12S,15R,16S,17R,18R)-15-(furan-3-yl)-10,17,18-trihydroxy-2,7,7,11,16-pentamethyl-6-oxatetracyclo[9.7.0.0^{2,8}.0^{12,16}]octadec-3-ene-5,13-dione

Traditional Name

(1R,2R,8R,10R,11R,12S,15R,16S,17R,18R)-15-(furan-3-yl)-10,17,18-trihydroxy-2,7,7,11,16-pentamethyl-6-oxatetracyclo[9.7.0.0^{2,8}.0^{12,16}]octadec-3-ene-5,13-dione

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])[C@]([H])(O[H])[C@@]2(C([H])([H])[H])[C@]([H])(C3=C([H])OC([H])=C3[H])C([H])([H])C(=O)[C@@]2([H])[C@]2(C([H])([H])[H])[C@]([H])(O[H])C([H])([H])[C@]3([H])[C@@](C([H])=C([H])C(=O)OC3(C([H])([H])[H])C([H])([H])[H])(C([H])([H])[H])[C@@]12[H]

InChI Identifier

InChI=1S/C26H34O7/c1-23(2)16-11-17(28)26(5)20-15(27)10-14(13-7-9-32-12-13)25(20,4)22(31)19(30)21(26)24(16,3)8-6-18(29)33-23/h6-9,12,14,16-17,19-22,28,30-31H,10-11H2,1-5H3/t14-,16-,17+,19+,20+,21+,22-,24-,25-,26-/m0/s1

InChI Key

ZKJDMXKOBXJDDB-MGJCYGGASA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Aphanamixis grandifolia	JEOL database	Zhang, Y., et al, J. Nat. Prod. 76, 1191 (2013)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as limonoids. These are highly oxygenated, modified terpenoids with a prototypical structure either containing or derived from a precursor with a 4,4,8-trimethyl-17-furanylsteroid skeleton. All naturally occurring citrus limonoids contain a furan ring attached to the D-ring, at C-17, as well as oxygen containing functional groups at C-3, C-4, C-7, C-16 and C-17.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Limonoids

Alternative Parents

Substituents

Limonoid skeleton
Cyclic alcohol
Furan
Heteroaromatic compound
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Ketone
Lactone
Secondary alcohol
Carboxylic acid derivative
Oxacycle
Organoheterocyclic compound
Polyol
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Carbonyl group
Alcohol
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	2.68	ALOGPS
logP	1.68	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	13.46	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	117.2 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	120.04 m³·mol⁻¹	ChemAxon
Polarizability	48.53 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

29784804

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

71726251

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Authors unspecified: Childhood Cancer Genomics (PDQ(R)): Health Professional Version. 2002. [PubMed:27466641 ]
Authors unspecified: Thyroid Cancer Screening (PDQ(R)): Patient Version. 2002. [PubMed:29437326 ]
Authors unspecified: Childhood Vascular Tumors Treatment (PDQ(R)): Patient Version. 2002. [PubMed:27253005 ]
Authors unspecified: Stomach (Gastric) Cancer Prevention (PDQ(R)): Patient Version. 2002. [PubMed:26389468 ]
Authors unspecified: Childhood Central Nervous System Atypical Teratoid/Rhabdoid Tumor Treatment (PDQ(R)): Health Professional Version. 2002. [PubMed:26389426 ]
Zhang, Y., et al. (2013). Zhang, Y., et al, J. Nat. Prod. 76, 1191 (2013). J. Nat. Prod..

Showing NP-Card for aphanalide I (NP0043482)

MOL for NP0043482 (aphanalide I)

3D MOL for NP0043482 (aphanalide I)

3D SDF for NP0043482 (aphanalide I)

3D-SDF for NP0043482 (aphanalide I)

PDB for NP0043482 (aphanalide I)

3D PDB for NP0043482 (aphanalide I)

SMILES for NP0043482 (aphanalide I)

INCHI for NP0043482 (aphanalide I)

Structure for NP0043482 (aphanalide I)

3D Structure for NP0043482 (aphanalide I)