NP-MRD: Showing NP-Card for (1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid (NP0160847)

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Record Information

Version

2.0

Created at

2022-09-02 18:53:46 UTC

Updated at

2022-09-02 18:53:46 UTC

NP-MRD ID

NP0160847

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid

Description

Rubiarbonone F belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. (1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid is found in Rubia yunnanensis. Based on a literature review very few articles have been published on Rubiarbonone F.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022220532D          

 35 39  0  0  1  0            999 V2000
    7.4687    1.1499    0.0000 C   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


  Mrv1652309022220532D          

 35 39  0  0  1  0            999 V2000
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   -0.4580    1.4271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4685    1.9434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1378    1.1206    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5611    1.8287    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3860    1.8162    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8093    2.5243    0.0000 O   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
  4  2  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  6  1  6  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
  8 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  1  6  0  0  0
 18 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
 23 32  1  0  0  0  0
 32 33  1  6  0  0  0
 33 34  1  0  0  0  0
 17 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0160847

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)[C@@H]1C[C@@H](O)[C@H]2[C@]1(CC[C@@]1(C)[C@@H]3[C@@H](O)C[C@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]21C)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O5/c1-16(2)18-14-20(32)24-29(7)11-8-17-23(28(29,6)12-13-30(18,24)25(34)35)19(31)15-21-26(3,4)22(33)9-10-27(17,21)5/h8,16,18-21,23-24,31-32H,9-15H2,1-7H3,(H,34,35)/t18-,19-,20+,21-,23-,24+,27+,28-,29+,30+/m0/s1

> <INCHI_KEY>
AFMHRCRCZJKBKZ-LPYXLCIUSA-N

> <FORMULA>
C30H46O5

> <MOLECULAR_WEIGHT>
486.693

> <EXACT_MASS>
486.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
56.23096422292034

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5R,6S,8R,9R,10R,14S,19R,21S)-8,21-dihydroxy-2,10,14,18,18-pentamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene-5-carboxylic acid

> <ALOGPS_LOGP>
4.55

> <JCHEM_LOGP>
4.527803521333334

> <ALOGPS_LOGS>
-4.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.912138471110573

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.552152048120911

> <JCHEM_PKA_STRONGEST_BASIC>
-0.4236045483413039

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
136.0607

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.43e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,6S,8R,9R,10R,14S,19R,21S)-8,21-dihydroxy-6-isopropyl-2,10,14,18,18-pentamethyl-17-oxopentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene-5-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      13.941   2.146   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.484   2.645   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.187   4.156   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.324   1.632   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.462   0.098   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.046  -0.507   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       9.703  -2.008   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.033   0.653   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.823   1.975   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.747   3.207   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.142   4.623   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      11.395   4.604   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.073   3.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.534   3.343   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.743   2.022   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.994   3.367   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.204   2.045   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.413   0.723   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.163  -0.622   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.703  -0.645   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.493   0.676   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.243  -0.669   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.874   0.747   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.623  -0.599   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.083  -0.575   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.543  -0.552   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.206   0.793   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.746   0.817   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.584   2.115   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.855   2.664   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       0.875   3.628   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.124   2.092   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.914   3.414   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.454   3.390   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       5.244   4.712   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   21                                                  
CONECT    9    8    4   10   13                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17   21                                             
CONECT   16   15                                                            
CONECT   17   15   18   34                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    8   15   22                                             
CONECT   22   21                                                            
CONECT   23   18   24   25   32                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31   32                                             
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   29   23   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33   17   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₆O₅

Average Mass

486.6930 Da

Monoisotopic Mass

486.33452 Da

IUPAC Name

(1S,2S,5R,6S,8R,9R,10R,14S,19R,21S)-8,21-dihydroxy-2,10,14,18,18-pentamethyl-17-oxo-6-(propan-2-yl)pentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene-5-carboxylic acid

Traditional Name

(1S,2S,5R,6S,8R,9R,10R,14S,19R,21S)-8,21-dihydroxy-6-isopropyl-2,10,14,18,18-pentamethyl-17-oxopentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene-5-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@@H]1C[C@@H](O)[C@H]2[C@]1(CC[C@@]1(C)[C@@H]3[C@@H](O)C[C@H]4C(C)(C)C(=O)CC[C@]4(C)C3=CC[C@]21C)C(O)=O

InChI Identifier

InChI=1S/C30H46O5/c1-16(2)18-14-20(32)24-29(7)11-8-17-23(28(29,6)12-13-30(18,24)25(34)35)19(31)15-21-26(3,4)22(33)9-10-27(17,21)5/h8,16,18-21,23-24,31-32H,9-15H2,1-7H3,(H,34,35)/t18-,19-,20+,21-,23-,24+,27+,28-,29+,30+/m0/s1

InChI Key

AFMHRCRCZJKBKZ-LPYXLCIUSA-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
Rubia yunnanensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
18-hydroxysteroid
18-oxosteroid
15-hydroxysteroid
1-hydroxysteroid
Hydroxysteroid
Oxosteroid
Delta-5-steroid
Steroid
Cyclic alcohol
Cyclic ketone
Ketone
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Alcohol
Carbonyl group
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic 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	4.55	ALOGPS
logP	4.53	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	4.55	ChemAxon
pKa (Strongest Basic)	-0.42	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	136.06 m³·mol⁻¹	ChemAxon
Polarizability	56.23 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

C00046362

Chemspider ID

9115094

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10939859

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid (NP0160847)

MOL for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

3D MOL for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

3D SDF for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

3D-SDF for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

PDB for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

3D PDB for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

SMILES for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

INCHI for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

Structure for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)

3D Structure for NP0160847 ((1r,3s,3ar,5as,5bs,6s,7ar,11as,13ar,13br)-1,6-dihydroxy-3-isopropyl-5a,8,8,11a,13a-pentamethyl-9-oxo-1h,2h,3h,4h,5h,5bh,6h,7h,7ah,10h,11h,13h,13bh-cyclopenta[a]chrysene-3a-carboxylic acid)