NP-MRD: Showing NP-Card for (+)-Axillaridine A (NP0082933)

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Record Information

Version

2.0

Created at

2022-04-29 04:00:24 UTC

Updated at

2022-04-29 04:00:24 UTC

NP-MRD ID

NP0082933

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Axillaridine A

Description

Axillaridine A belongs to the class of organic compounds known as oxosteroids. These are steroid derivatives carrying a C=O group attached to steroid skeleton. (+)-Axillaridine A is found in Pachysandra axillaris, Pachysandra procumbens and Sarcococca saligna. (+)-Axillaridine A was first documented in 2021 (PMID: 32208773). Based on a literature review very few articles have been published on Axillaridine A.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292206002D          

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 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 28 33  1  0  0  0  0
 19 34  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0082933

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC[C@H]4C(=O)C(NC(=O)C5=CC=CC=C5)=CC[C@]4(C)[C@H]3CC[C@]12C)N(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H42N2O2/c1-19(32(4)5)22-13-14-23-21-11-12-25-27(33)26(31-28(34)20-9-7-6-8-10-20)16-18-30(25,3)24(21)15-17-29(22,23)2/h6-10,16,19,21-25H,11-15,17-18H2,1-5H3,(H,31,34)/t19-,21-,22+,23-,24-,25-,29+,30+/m0/s1

> <INCHI_KEY>
ZMAOKPMWBVUQPK-IWDJEAQTSA-N

> <FORMULA>
C30H42N2O2

> <MOLECULAR_WEIGHT>
462.678

> <EXACT_MASS>
462.3246286

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
56.2239303847397

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(1S,2R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-5-yl]benzamide

> <ALOGPS_LOGP>
5.65

> <JCHEM_LOGP>
5.4666575889999995

> <ALOGPS_LOGS>
-6.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.357825228371212

> <JCHEM_PKA_STRONGEST_BASIC>
9.600221078820056

> <JCHEM_POLAR_SURFACE_AREA>
49.410000000000004

> <JCHEM_REFRACTIVITY>
139.4919

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.11e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-[(1S,2R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-5-yl]benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

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  N   UNK     0      11.407  -1.269   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.988   0.157   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.302  -2.907   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  O   UNK     0       0.287   3.667   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0      -1.698   1.312   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      -2.691   0.135   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.168  -1.314   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -4.207   0.406   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.200  -0.771   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.716  -0.500   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -7.239   0.948   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -6.246   2.125   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -4.730   1.854   0.000  0.00  0.00           C+0
HETATM   34  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   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10                                                            
CONECT   15    5                                                            
CONECT   16    3   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   23                                                  
CONECT   19   18    2   20   34                                             
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   25                                                  
CONECT   23   22   18   24                                                  
CONECT   24   23                                                            
CONECT   25   22   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   33                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   28                                                       
CONECT   34   19                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₂N₂O₂

Average Mass

462.6780 Da

Monoisotopic Mass

462.32463 Da

IUPAC Name

N-[(1S,2R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-5-yl]benzamide

Traditional Name

N-[(1S,2R,7R,10S,11S,14S,15S)-14-[(1S)-1-(dimethylamino)ethyl]-2,15-dimethyl-6-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-4-en-5-yl]benzamide

CAS Registry Number

Not Available

SMILES

C[C@@H]([C@H]1CC[C@H]2[C@@H]3CC[C@H]4C(=O)C(NC(=O)C5=CC=CC=C5)=CC[C@]4(C)[C@H]3CC[C@]12C)N(C)C

InChI Identifier

InChI=1S/C30H42N2O2/c1-19(32(4)5)22-13-14-23-21-11-12-25-27(33)26(31-28(34)20-9-7-6-8-10-20)16-18-30(25,3)24(21)15-17-29(22,23)2/h6-10,16,19,21-25H,11-15,17-18H2,1-5H3,(H,31,34)/t19-,21-,22+,23-,24-,25-,29+,30+/m0/s1

InChI Key

ZMAOKPMWBVUQPK-IWDJEAQTSA-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 axillaris	LOTUS Database	35616633
Pachysandra procumbens	Plant	KNApSAcK
Sarcococca saligna	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
Benzamide
Benzoic acid or derivatives
Benzoyl
Cyclohexenone
Benzenoid
Monocyclic benzene moiety
Tertiary aliphatic amine
Tertiary amine
Secondary carboxylic acid amide
Amino acid or derivatives
Carboxamide group
Ketone
Carboxylic acid derivative
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organonitrogen compound
Organooxygen compound
Amine
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	5.65	ALOGPS
logP	5.47	ChemAxon
logS	-6.2	ALOGPS
pKa (Strongest Acidic)	13.36	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	139.49 m³·mol⁻¹	ChemAxon
Polarizability	56.22 Å³	ChemAxon
Number of Rings	5	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

C00049910

Chemspider ID

2274765

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3004425

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang Y, Li Y, Huang S, Cui Y, Zhang H, Huang W, Deng C, Wang W, Song X: Two new pregnane alkaloids from Pachysandra terminalis Sieb. et Zucc. Nat Prod Res. 2021 Nov;35(21):3888-3894. doi: 10.1080/14786419.2020.1744143. Epub 2020 Mar 25. [PubMed:32208773 ]

Showing NP-Card for (+)-Axillaridine A (NP0082933)

MOL for NP0082933 ((+)-Axillaridine A)

3D MOL for NP0082933 ((+)-Axillaridine A)

3D SDF for NP0082933 ((+)-Axillaridine A)

3D-SDF for NP0082933 ((+)-Axillaridine A)

PDB for NP0082933 ((+)-Axillaridine A)

3D PDB for NP0082933 ((+)-Axillaridine A)

SMILES for NP0082933 ((+)-Axillaridine A)

INCHI for NP0082933 ((+)-Axillaridine A)

Structure for NP0082933 ((+)-Axillaridine A)

3D Structure for NP0082933 ((+)-Axillaridine A)