NP-MRD: Showing NP-Card for (1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one (NP0168437)

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Record Information

Version

2.0

Created at

2022-09-03 04:15:06 UTC

Updated at

2022-09-03 04:15:06 UTC

NP-MRD ID

NP0168437

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one

Description

Stigmasta-4-22-dien-3-one belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24. (1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one is found in Amphilectus fucorum, Conium maculatum, Cymodocea nodosa, Duhaldea cappa, Ephedra distachya, Friesodielsia velutina, Frullania brasiliensis, Harrisonia abyssinica, Laggera alata, Lophanthera lactescens, Magnolia kachirachirai, Nelumbo nucifera, Oreocnide frutescens, Pellia epiphylla, Ravenia spectabilis and Rhinacanthus nasutus. Stigmasta-4-22-dien-3-one is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241221392D          

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M  END

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M  END


  Mrv0541 02241221392D          

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 23 25  1  0  0  0  0
 17 26  1  6  0  0  0
  9 27  1  1  0  0  0
  5 28  1  1  0  0  0
  5 29  1  0  0  0  0
 29 30  1  0  0  0  0
  2 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0168437

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H](C(C)C)\C=C\[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C29H46O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h8-9,18-21,24-27H,7,10-17H2,1-6H3/b9-8+/t20-,21-,24+,25-,26+,27+,28+,29-/m1/s1

> <INCHI_KEY>
MKGZDUKUQPPHFM-LPJPOILFSA-N

> <FORMULA>
C29H46O

> <MOLECULAR_WEIGHT>
410.6749

> <EXACT_MASS>
410.354866094

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
52.41760295108885

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,10S,11S,14R,15R)-14-[(2R,3E,5S)-5-ethyl-6-methylhept-3-en-2-yl]-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-6-en-5-one

> <ALOGPS_LOGP>
6.47

> <JCHEM_LOGP>
8.049801083333335

> <ALOGPS_LOGS>
-7.35

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.087824195598667

> <JCHEM_PKA_STRONGEST_BASIC>
-4.8174402351669805

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
129.83129999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.85e-05 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,10S,11S,14R,15R)-14-[(2R,3E,5S)-5-ethyl-6-methylhept-3-en-2-yl]-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-6-en-5-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0      -1.698  -4.392   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.182  -4.121   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.811  -5.298   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.326  -5.027   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.850  -3.579   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.366  -3.308   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.889  -1.859   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.405  -1.588   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.397  -2.766   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.937  -2.816   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.365  -4.295   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.090  -5.159   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.874  -4.214   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.358  -4.485   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.835  -5.934   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.319  -6.205   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.882  -1.600   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      11.407  -1.811   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.353  -0.595   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.878  -0.805   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      14.823   0.410   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      16.349   0.200   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      14.458  -2.232   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.984  -2.443   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.513  -3.448   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.302  -0.173   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       8.069  -1.380   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       3.373  -2.131   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.857  -2.402   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.341  -2.673   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   16                                                  
CONECT    5    4    6   28   29                                             
CONECT    6    5    7   14                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   13   27                                             
CONECT   10    9   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    9   14                                                  
CONECT   14   13    6   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15    4                                                       
CONECT   17   10   18   26                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   23                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23   20   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   17                                                            
CONECT   27    9                                                            
CONECT   28    5                                                            
CONECT   29    5   30                                                       
CONECT   30   29    2                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₆O

Average Mass

410.6749 Da

Monoisotopic Mass

410.35487 Da

IUPAC Name

(1S,2R,10S,11S,14R,15R)-14-[(2R,3E,5S)-5-ethyl-6-methylhept-3-en-2-yl]-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-6-en-5-one

Traditional Name

(1S,2R,10S,11S,14R,15R)-14-[(2R,3E,5S)-5-ethyl-6-methylhept-3-en-2-yl]-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-6-en-5-one

CAS Registry Number

Not Available

SMILES

CC[C@@H](C(C)C)\C=C\[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C

InChI Identifier

InChI=1S/C29H46O/c1-7-21(19(2)3)9-8-20(4)25-12-13-26-24-11-10-22-18-23(30)14-16-28(22,5)27(24)15-17-29(25,26)6/h8-9,18-21,24-27H,7,10-17H2,1-6H3/b9-8+/t20-,21-,24+,25-,26+,27+,28+,29-/m1/s1

InChI Key

MKGZDUKUQPPHFM-LPJPOILFSA-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
Amphilectus fucorum	LOTUS Database	35616633
Conium maculatum	LOTUS Database	35616633
Cymodocea nodosa	LOTUS Database	35616633
Duhaldea cappa	LOTUS Database	35616633
Ephedra distachya	LOTUS Database	35616633
Friesodielsia velutina	LOTUS Database	35616633
Frullania brasiliensis	LOTUS Database	35616633
Harrisonia abyssinica	LOTUS Database	35616633
Laggera alata	LOTUS Database	35616633
Lophanthera lactescens	LOTUS Database	35616633
Magnolia kachirachirai	LOTUS Database	35616633
Nelumbo nucifera	LOTUS Database	35616633
Oreocnide frutescens	LOTUS Database	35616633
Pellia epiphylla	LOTUS Database	35616633
Ravenia spectabilis	LOTUS Database	35616633
Rhinacanthus nasutus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Stigmastanes and derivatives

Direct Parent

Stigmastanes and derivatives

Alternative Parents

Substituents

Triterpenoid
Stigmastane-skeleton
Oxosteroid
3-oxosteroid
3-oxo-delta-4-steroid
Delta-4-steroid
Cyclohexenone
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	6.47	ALOGPS
logP	8.05	ChemAxon
logS	-7.4	ALOGPS
pKa (Strongest Acidic)	19.09	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	17.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	129.83 m³·mol⁻¹	ChemAxon
Polarizability	52.42 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB005657

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

6442194

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one (NP0168437)

MOL for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

3D MOL for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

3D SDF for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

3D-SDF for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

PDB for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

3D PDB for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

SMILES for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

INCHI for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

Structure for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)

3D Structure for NP0168437 ((1r,3as,3bs,9ar,9bs,11ar)-1-[(2r,3e,5s)-5-ethyl-6-methylhept-3-en-2-yl]-9a,11a-dimethyl-1h,2h,3h,3ah,3bh,4h,5h,8h,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-one)