NP-MRD: Showing NP-Card for 12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one (NP0227989)

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Record Information

Version

2.0

Created at

2022-09-06 07:29:37 UTC

Updated at

2022-09-06 07:29:37 UTC

NP-MRD ID

NP0227989

Secondary Accession Numbers

None

Natural Product Identification

Common Name

12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one

Description

Gomisin D belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. 12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one is found in Kadsura coccinea and Schisandra chinensis. Gomisin D is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004171512582D          

 38 42  0  0  0  0            999 V2000
   -0.9086    1.4214    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1877    1.8226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.2152    0.1505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9892   -0.6430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4546   -0.0242    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1533004171512582D          

 38 42  0  0  0  0            999 V2000
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    1.2410    1.8003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2540    2.6252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9748    3.0264    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
  3  4  2  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  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
  6 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 24 31  2  0  0  0  0
 17 31  1  0  0  0  0
 31 32  1  0  0  0  0
  5 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 33 36  2  0  0  0  0
  3 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0227989

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC2=C(C(OC)=C1OC)C1=C3CC(C)C(C)(O)C2OC(=O)C(C)(O)C(C)COC1=C1OCOC1=C3

> <INCHI_IDENTIFIER>
InChI=1S/C28H34O10/c1-13-8-15-9-18-22(37-12-36-18)24-19(15)20-16(10-17(32-5)21(33-6)23(20)34-7)25(27(13,3)30)38-26(29)28(4,31)14(2)11-35-24/h9-10,13-14,25,30-31H,8,11-12H2,1-7H3

> <INCHI_KEY>
VLLFEMVDMFTBHG-UHFFFAOYSA-N

> <FORMULA>
C28H34O10

> <MOLECULAR_WEIGHT>
530.57

> <EXACT_MASS>
530.215197295

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
54.43917009412681

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one

> <ALOGPS_LOGP>
2.97

> <JCHEM_LOGP>
3.0414665026666654

> <ALOGPS_LOGS>
-4.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.691180446540994

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.288337828168418

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3793700141988943

> <JCHEM_POLAR_SURFACE_AREA>
122.14000000000003

> <JCHEM_REFRACTIVITY>
134.908

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.87e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -1.696   2.653   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -0.350   3.402   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       0.978   2.176   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.947   1.072   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.268   0.281   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.847  -1.200   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.849  -0.045   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.496   1.454   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.041   1.538   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.010   2.906   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.530   2.917   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.517   4.365   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       2.224   4.067   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.666   5.283   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.762   3.984   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       5.561   3.276   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.886   1.930   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.426   1.905   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.474   3.034   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       9.871   2.385   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       9.686   0.856   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       8.175   0.560   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.384  -0.762   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.844  -0.738   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.422  -2.219   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.077  -2.968   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       4.254  -4.497   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.596  -2.546   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.204  -3.205   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.272  -4.051   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.095   0.608   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.614   1.030   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.638   2.570   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       4.984   3.319   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       5.008   4.859   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.317   3.360   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.341   4.900   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0       3.686   5.649   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7   28                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12   13                                             
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13   10   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   31                                                  
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   18   23                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   31                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26    6   29   30                                             
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   24   17   32                                                  
CONECT   32   31    5   33                                                  
CONECT   33   32   34   36                                                  
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   33    3   37                                                  
CONECT   37   36   38                                                       
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₄O₁₀

Average Mass

530.5700 Da

Monoisotopic Mass

530.21520 Da

IUPAC Name

12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one

Traditional Name

12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one

CAS Registry Number

Not Available

SMILES

COC1=CC2=C(C(OC)=C1OC)C1=C3CC(C)C(C)(O)C2OC(=O)C(C)(O)C(C)COC1=C1OCOC1=C3

InChI Identifier

InChI=1S/C28H34O10/c1-13-8-15-9-18-22(37-12-36-18)24-19(15)20-16(10-17(32-5)21(33-6)23(20)34-7)25(27(13,3)30)38-26(29)28(4,31)14(2)11-35-24/h9-10,13-14,25,30-31H,8,11-12H2,1-7H3

InChI Key

VLLFEMVDMFTBHG-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

Species Name	Source	Reference
Kadsura coccinea	LOTUS Database	35616633
Schisandra chinensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

Hydrolyzable tannin
Dibenzocyclooctane lignan
Lignan lactone
Benzodioxole
Anisole
Alkyl aryl ether
Benzenoid
Tertiary alcohol
Lactone
Carboxylic acid ester
Organoheterocyclic compound
Oxacycle
Monocarboxylic acid or derivatives
Ether
Acetal
Carboxylic acid derivative
Organooxygen compound
Carbonyl group
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Alcohol
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	2.97	ALOGPS
logP	3.04	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	12.29	ChemAxon
pKa (Strongest Basic)	-3.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	122.14 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	134.91 m³·mol⁻¹	ChemAxon
Polarizability	54.44 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	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

75130910

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one (NP0227989)

MOL for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

3D MOL for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

3D SDF for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

3D-SDF for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

PDB for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

3D PDB for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

SMILES for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

INCHI for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

Structure for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)

3D Structure for NP0227989 (12,25-dihydroxy-18,19,20-trimethoxy-11,12,24,25-tetramethyl-4,6,9,14-tetraoxapentacyclo[13.7.3.0³,⁷.0⁸,²².0¹⁶,²¹]pentacosa-1(22),2,7,16(21),17,19-hexaen-13-one)