NP-MRD: Showing NP-Card for (3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione (NP0318927)

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Record Information

Version

2.0

Created at

2022-09-11 19:42:16 UTC

Updated at

2022-09-11 19:42:16 UTC

NP-MRD ID

NP0318927

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione

Description

Geoditin A belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. (3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione is found in Geodia japonica. (3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione was first documented in 2005 (PMID: 16253766). Based on a literature review a small amount of articles have been published on geoditin A (PMID: 22412813) (PMID: 20161972) (PMID: 17048627).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112221422D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309112221422D          

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M  END
> <DATABASE_ID>
NP0318927

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)\C=C\C(=O)C(\C)=C\C=C\C(\C)=C1/C(=O)C[C@@H]2[C@]1(C)CC[C@@H]1[C@]2(C)CCC(=O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C29H38O4/c1-18(21(31)12-11-20(3)30)9-8-10-19(2)26-22(32)17-24-28(6)16-14-25(33)27(4,5)23(28)13-15-29(24,26)7/h8-12,23-24H,13-17H2,1-7H3/b10-8+,12-11+,18-9+,26-19+/t23-,24-,28-,29-/m0/s1

> <INCHI_KEY>
LZZDDKOYYZTLIC-OGMVXUOOSA-N

> <FORMULA>
C29H38O4

> <MOLECULAR_WEIGHT>
450.619

> <EXACT_MASS>
450.277009704

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
53.00314101428076

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3Z,3aS,5aR,9aR,9bS)-3a,6,6,9a-tetramethyl-3-[(3E,5E,8E)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-dodecahydro-1H-cyclopenta[a]naphthalene-2,7-dione

> <JCHEM_LOGP>
5.974873496

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.788349130856094

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.25135471093414

> <JCHEM_PKA_STRONGEST_BASIC>
-4.812303771859597

> <JCHEM_POLAR_SURFACE_AREA>
68.28

> <JCHEM_REFRACTIVITY>
135.34279999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3Z,3aS,5aR,9aR,9bS)-3a,6,6,9a-tetramethyl-3-[(3E,5E,8E)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1H-cyclopenta[a]naphthalene-2,7-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      16.401  -6.514   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      16.674  -4.998   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      18.123  -4.477   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      15.497  -4.004   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      15.770  -2.488   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.594  -1.494   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      14.867   0.021   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      13.145  -2.016   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.872  -3.531   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.969  -1.021   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.520  -1.543   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.344  -0.549   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.895  -1.070   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.622  -2.586   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.719  -0.076   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.832   1.460   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       8.141   2.271   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.406   2.042   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.412   0.866   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.223  -0.443   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.167  -1.660   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.495  -1.800   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.956  -1.848   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.145  -0.539   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.606  -0.587   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.920  -2.095   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.824  -1.159   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.206   0.722   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -1.745   0.674   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.522   2.079   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.062   2.127   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.873   0.818   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.601   2.175   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   20                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18   20   32                                                  
CONECT   20   19   15   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   32                                                  
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   19   24   33                                             
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₃₈O₄

Average Mass

450.6190 Da

Monoisotopic Mass

450.27701 Da

IUPAC Name

(3Z,3aS,5aR,9aR,9bS)-3a,6,6,9a-tetramethyl-3-[(3E,5E,8E)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-dodecahydro-1H-cyclopenta[a]naphthalene-2,7-dione

Traditional Name

(3Z,3aS,5aR,9aR,9bS)-3a,6,6,9a-tetramethyl-3-[(3E,5E,8E)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1H-cyclopenta[a]naphthalene-2,7-dione

CAS Registry Number

Not Available

SMILES

CC(=O)\C=C\C(=O)C(\C)=C\C=C\C(\C)=C1/C(=O)C[C@@H]2[C@]1(C)CC[C@@H]1[C@]2(C)CCC(=O)C1(C)C

InChI Identifier

InChI=1S/C29H38O4/c1-18(21(31)12-11-20(3)30)9-8-10-19(2)26-22(32)17-24-28(6)16-14-25(33)27(4,5)23(28)13-15-29(24,26)7/h8-12,23-24H,13-17H2,1-7H3/b10-8+,12-11+,18-9+,26-19+/t23-,24-,28-,29-/m0/s1

InChI Key

LZZDDKOYYZTLIC-OGMVXUOOSA-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
Geodia japonica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Alpha-branched alpha,beta-unsaturated-ketone
Alpha,beta-unsaturated ketone
Enone
Acryloyl-group
Cyclic ketone
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
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	5.97	ChemAxon
pKa (Strongest Acidic)	19.25	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	68.28 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	135.34 m³·mol⁻¹	ChemAxon
Polarizability	53 Å³	ChemAxon
Number of Rings	3	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

C00043152

Chemspider ID

24701838

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

44575708

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liu WK, Ho JC, Che CT: Apoptotic activity of isomalabaricane triterpenes on human promyelocytic leukemia HL60 cells. Cancer Lett. 2005 Dec 8;230(1):102-10. doi: 10.1016/j.canlet.2004.12.034. Epub 2005 Jan 28. [PubMed:16253766 ]
Cheung FWK, Guo J, Ling YH, Che CT, Liu WK: Anti-melanogenic property of geoditin A in murine B16 melanoma cells. Mar Drugs. 2012 Feb;10(2):465-476. doi: 10.3390/md10020465. Epub 2012 Feb 16. [PubMed:22412813 ]
Cheung FW, Li C, Che CT, Liu BP, Wang L, Liu WK: Geoditin A induces oxidative stress and apoptosis on human colon HT29 cells. Mar Drugs. 2010 Jan 19;8(1):80-90. doi: 10.3390/md8010080. [PubMed:20161972 ]
Lu F, Lin WH: [Bioactive isomalabaricane triterpenes isolated from marine sponge Rhabdastrella aff. distincta]. Zhongguo Zhong Yao Za Zhi. 2006 Jun;31(11):894-8. [PubMed:17048627 ]
LOTUS database [Link]

Showing NP-Card for (3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione (NP0318927)

MOL for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

3D MOL for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

3D SDF for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

3D-SDF for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

PDB for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

3D PDB for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

SMILES for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

INCHI for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

Structure for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)

3D Structure for NP0318927 ((3z,3as,5ar,9ar,9bs)-3a,6,6,9a-tetramethyl-3-[(3e,5e,8e)-6-methyl-7,10-dioxoundeca-3,5,8-trien-2-ylidene]-hexahydro-1h-cyclopenta[a]naphthalene-2,7-dione)