NP-MRD: Showing NP-Card for n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid (NP0292732)

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Record Information

Version

2.0

Created at

2022-09-10 00:24:22 UTC

Updated at

2022-09-10 00:24:23 UTC

NP-MRD ID

NP0292732

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid

Description

Pachysamine M belongs to the class of organic compounds known as oxosteroids. These are steroid derivatives carrying a C=O group attached to steroid skeleton. n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid is found in Pachysandra axillaris. Pachysamine M is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251523442D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251523442D          

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 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
  2 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0292732

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C1CCC2C3CCC4C(=O)C(NC(=O)C=C(C)C)=CCC4(C)C3CCC12C)N(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C28H44N2O2/c1-17(2)16-25(31)29-24-13-15-28(5)22-12-14-27(4)20(18(3)30(6)7)10-11-21(27)19(22)8-9-23(28)26(24)32/h13,16,18-23H,8-12,14-15H2,1-7H3,(H,29,31)

> <INCHI_KEY>
FPBGDMGTAHIUMI-UHFFFAOYSA-N

> <FORMULA>
C28H44N2O2

> <MOLECULAR_WEIGHT>
440.672

> <EXACT_MASS>
440.340278665

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
53.87866030593382

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-{14-[1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-5-yl}-3-methylbut-2-enamide

> <ALOGPS_LOGP>
5.01

> <JCHEM_LOGP>
4.998772424000002

> <ALOGPS_LOGS>
-5.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.130533821084597

> <JCHEM_PKA_STRONGEST_BASIC>
9.600168869543337

> <JCHEM_POLAR_SURFACE_AREA>
49.410000000000004

> <JCHEM_REFRACTIVITY>
133.42459999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.14e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-{14-[1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-5-yl}-3-methylbut-2-enamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.377  -0.716   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.595  -6.083   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      16.362  -3.071   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      17.355  -4.248   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.832  -5.696   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      18.871  -3.977   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      19.864  -5.154   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      21.380  -4.883   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      19.341  -6.603   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       3.257  -5.652   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.676  -4.226   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   30                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   21                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   23                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10   17   18                                             
CONECT   17   16                                                            
CONECT   18   16    7   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20    3    6   22                                             
CONECT   22   21                                                            
CONECT   23   13   24                                                       
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30    2   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Value	Source
N-{14-[1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-5-yl}-3-methylbut-2-enimidate	Generator

Chemical Formula

C₂₈H₄₄N₂O₂

Average Mass

440.6720 Da

Monoisotopic Mass

440.34028 Da

IUPAC Name

N-{14-[1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-5-yl}-3-methylbut-2-enamide

Traditional Name

N-{14-[1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadec-4-en-5-yl}-3-methylbut-2-enamide

CAS Registry Number

Not Available

SMILES

CC(C1CCC2C3CCC4C(=O)C(NC(=O)C=C(C)C)=CCC4(C)C3CCC12C)N(C)C

InChI Identifier

InChI=1S/C28H44N2O2/c1-17(2)16-25(31)29-24-13-15-28(5)22-12-14-27(4)20(18(3)30(6)7)10-11-21(27)19(22)8-9-23(28)26(24)32/h13,16,18-23H,8-12,14-15H2,1-7H3,(H,29,31)

InChI Key

FPBGDMGTAHIUMI-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
Pachysandra axillaris	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oxosteroids. These are steroid derivatives carrying a C=O group attached to steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Oxosteroids

Direct Parent

Oxosteroids

Alternative Parents

Substituents

22-azasteroid
Pregnane-skeleton
Pregnane-type alkaloid
Steroidal alkaloid
Oxosteroid
4-oxosteroid
Azasteroid
Alkaloid or derivatives
Cyclohexenone
N-acyl-amine
Tertiary aliphatic amine
Tertiary amine
Amino acid or derivatives
Secondary carboxylic acid amide
Carboxamide group
Ketone
Carboxylic acid derivative
Organic oxide
Organonitrogen compound
Organooxygen compound
Amine
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
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	5.01	ALOGPS
logP	5	ChemAxon
logS	-5.6	ALOGPS
pKa (Strongest Acidic)	13.13	ChemAxon
pKa (Strongest Basic)	9.6	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.41 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	133.42 m³·mol⁻¹	ChemAxon
Polarizability	53.88 Å³	ChemAxon
Number of Rings	4	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

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

75244638

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid (NP0292732)

MOL for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

3D MOL for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

3D SDF for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

3D-SDF for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

PDB for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

3D PDB for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

SMILES for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

INCHI for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

Structure for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)

3D Structure for NP0292732 (n-{1-[1-(dimethylamino)ethyl]-9a,11a-dimethyl-6-oxo-1h,2h,3h,3ah,3bh,4h,5h,5ah,9h,9bh,10h,11h-cyclopenta[a]phenanthren-7-yl}-3-methylbut-2-enimidic acid)