NP-MRD: Showing NP-Card for Epipachysamine D (NP0082786)

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Record Information

Version

2.0

Created at

2022-04-29 03:52:31 UTC

Updated at

2022-04-29 03:52:31 UTC

NP-MRD ID

NP0082786

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Epipachysamine D

Description

Epipachysamine D belongs to the class of organic compounds known as azasteroids and derivatives. These are steroid derivatives in which one carbon atom in the steroidal skeleton has been substituted with a nitrogen atom. Epipachysamine D is found in Pachysandra procumbens and Sarcococca saligna . Based on a literature review very few articles have been published on Epipachysamine D.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292205522D          

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M  END

     RDKit          3D

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 18 23  1  0  0  0  0
 22 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 27 32  1  0  0  0  0
 19 33  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0082786

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)NC(=O)C1=CC=CC=C1)N(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H46N2O/c1-20(32(4)5)25-13-14-26-24-12-11-22-19-23(31-28(33)21-9-7-6-8-10-21)15-17-29(22,2)27(24)16-18-30(25,26)3/h6-10,20,22-27H,11-19H2,1-5H3,(H,31,33)/t20-,22-,23-,24-,25+,26-,27-,29-,30+/m0/s1

> <INCHI_KEY>
SFKPSOAYNYYOLN-IBWRYCSWSA-N

> <FORMULA>
C30H46N2O

> <MOLECULAR_WEIGHT>
450.711

> <EXACT_MASS>
450.361014109

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
55.70860246901056

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1S,2S,5S,7S,10R,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]benzamide

> <ALOGPS_LOGP>
5.80

> <JCHEM_LOGP>
6.054322911333336

> <ALOGPS_LOGS>
-6.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.098126609543659

> <JCHEM_PKA_STRONGEST_BASIC>
10.3002900703144

> <JCHEM_POLAR_SURFACE_AREA>
32.34

> <JCHEM_REFRACTIVITY>
137.43339999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.36e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1S,2S,5S,7S,10R,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]benzamide

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.302  -2.907   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      11.407  -1.269   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.988   0.157   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.069  -1.700   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -1.698   1.312   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0      -2.691   0.135   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -2.168  -1.314   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -4.207   0.406   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -5.200  -0.771   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.716  -0.500   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -7.239   0.948   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -6.246   2.125   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -4.730   1.854   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   19                                                  
CONECT    3    2    4   16                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7   15                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    7   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    5                                                            
CONECT   16    3   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18    2   20   33                                             
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22   18                                                       
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   27                                                       
CONECT   33   19                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₆N₂O

Average Mass

450.7110 Da

Monoisotopic Mass

450.36101 Da

IUPAC Name

N-[(1S,2S,5S,7S,10R,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]benzamide

Traditional Name

N-[(1S,2S,5S,7S,10R,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-5-yl]benzamide

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)NC(=O)C1=CC=CC=C1)N(C)C

InChI Identifier

InChI=1S/C30H46N2O/c1-20(32(4)5)25-13-14-26-24-12-11-22-19-23(31-28(33)21-9-7-6-8-10-21)15-17-29(22,2)27(24)16-18-30(25,26)3/h6-10,20,22-27H,11-19H2,1-5H3,(H,31,33)/t20-,22-,23-,24-,25+,26-,27-,29-,30+/m0/s1

InChI Key

SFKPSOAYNYYOLN-IBWRYCSWSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 procumbens	LOTUS Database	35616633
Sarcococca saligna	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as azasteroids and derivatives. These are steroid derivatives in which one carbon atom in the steroidal skeleton has been substituted with a nitrogen atom.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Azasteroids and derivatives

Direct Parent

Azasteroids and derivatives

Alternative Parents

Substituents

22-azasteroid
Pregnane-skeleton
Pregnane-type alkaloid
Steroidal alkaloid
Azasteroid
Benzamide
Benzoic acid or derivatives
Alkaloid or derivatives
Benzoyl
Monocyclic benzene moiety
Benzenoid
Tertiary aliphatic amine
Carboxamide group
Amino acid or derivatives
Secondary carboxylic acid amide
Tertiary amine
Carboxylic acid derivative
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Amine
Organic oxide
Organic oxygen compound
Organic nitrogen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic 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	5.8	ALOGPS
logP	6.05	ChemAxon
logS	-6.5	ALOGPS
pKa (Strongest Acidic)	15.1	ChemAxon
pKa (Strongest Basic)	10.3	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.34 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	137.43 m³·mol⁻¹	ChemAxon
Polarizability	55.71 Å³	ChemAxon
Number of Rings	5	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

Not Available

KNApSAcK ID

C00049718

Chemspider ID

8609350

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10433924

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Epipachysamine D (NP0082786)

MOL for NP0082786 (Epipachysamine D)

3D MOL for NP0082786 (Epipachysamine D)

3D SDF for NP0082786 (Epipachysamine D)

3D-SDF for NP0082786 (Epipachysamine D)

PDB for NP0082786 (Epipachysamine D)

3D PDB for NP0082786 (Epipachysamine D)

SMILES for NP0082786 (Epipachysamine D)

INCHI for NP0082786 (Epipachysamine D)

Structure for NP0082786 (Epipachysamine D)

3D Structure for NP0082786 (Epipachysamine D)