NP-MRD: Showing NP-Card for Paxillarine A (NP0066469)

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Record Information

Version

2.0

Created at

2022-04-28 10:44:13 UTC

Updated at

2022-04-28 10:44:13 UTC

NP-MRD ID

NP0066469

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Paxillarine A

Description

(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-6-yl acetate belongs to the class of organic compounds known as 16-oxosteroids. These are steroid derivatives carrying a C=O group at the 16-position of the steroid skeleton. Paxillarine A is found in Pachysandra axillaris and Pachysandra axillaris FRANCH. Based on a literature review very few articles have been published on (1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]Heptadecan-6-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282212442D          

 39 43  0  0  1  0            999 V2000
    4.2475    2.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282212442D          

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    0.0962    0.8215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3626    1.0042    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8637    2.7283    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5528    3.4925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6810    2.6155    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1873    3.2668    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9919    1.8513    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1073    2.8462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6232    2.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2763   -0.0289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7444   -0.6596    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0247   -1.4355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9323   -0.5144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3399    1.2325    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6202    0.4566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0884   -0.1741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4323    0.3114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9641    0.9421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7763    0.7969    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0566    0.0209    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5247   -0.6098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7126   -0.4646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8717    1.8632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
  4 10  1  6  0  0  0
  8 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
  7 14  1  6  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 11 17  1  6  0  0  0
 16 18  1  6  0  0  0
 15 19  1  6  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 12 24  1  1  0  0  0
  5 25  1  6  0  0  0
  3 26  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
  2 30  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
 30 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0066469

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C33H50N2O4/c1-20(34(5)6)29-28(37)19-26-23-13-14-25-30(39-21(2)36)27(35(7)31(38)22-11-9-8-10-12-22)16-18-32(25,3)24(23)15-17-33(26,29)4/h8-12,20,23-30,37H,13-19H2,1-7H3/t20-,23+,24-,25-,26-,27+,28-,29-,30+,32+,33+/m0/s1

> <INCHI_KEY>
CEFWIVSCALJZMU-ZZGCFVDSSA-N

> <FORMULA>
C33H50N2O4

> <MOLECULAR_WEIGHT>
538.773

> <EXACT_MASS>
538.377058098

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
89

> <JCHEM_AVERAGE_POLARIZABILITY>
62.673433825772804

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-6-yl acetate

> <ALOGPS_LOGP>
4.45

> <JCHEM_LOGP>
4.377012710333334

> <ALOGPS_LOGS>
-5.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.874539925381065

> <JCHEM_PKA_STRONGEST_BASIC>
9.770565366043432

> <JCHEM_POLAR_SURFACE_AREA>
70.08000000000001

> <JCHEM_REFRACTIVITY>
154.33679999999993

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.80e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-6-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.544   1.875   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.032   6.519   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -3.138   4.882   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0      -4.083   6.098   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.718   3.456   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       7.982  -0.054   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       6.990  -1.231   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       7.513  -2.680   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.474  -0.960   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       9.968   2.301   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0      10.491   0.852   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       9.498  -0.325   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      12.007   0.581   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.000   1.759   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.516   1.487   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      15.039   0.039   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      14.046  -1.138   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      12.530  -0.867   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      10.961   3.478   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   30                                                  
CONECT    3    2    4   26                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   25                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12   17                                                  
CONECT   12   11   13   15   24                                             
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16   19                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   11                                                       
CONECT   18   16                                                            
CONECT   19   15   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   12                                                            
CONECT   25    5                                                            
CONECT   26    3   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30    2   31   39                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
CONECT   39   30                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Value	Source
(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(Dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0,.0,]heptadecan-6-yl acetic acid	Generator

Chemical Formula

C₃₃H₅₀N₂O₄

Average Mass

538.7730 Da

Monoisotopic Mass

538.37706 Da

IUPAC Name

(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-6-yl acetate

Traditional Name

(1S,2R,5R,6R,7R,10R,11S,13S,14S,15R)-14-[(1S)-1-(dimethylamino)ethyl]-13-hydroxy-2,15-dimethyl-5-(N-methylbenzamido)tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-6-yl acetate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C33H50N2O4/c1-20(34(5)6)29-28(37)19-26-23-13-14-25-30(39-21(2)36)27(35(7)31(38)22-11-9-8-10-12-22)16-18-32(25,3)24(23)15-17-33(26,29)4/h8-12,20,23-30,37H,13-19H2,1-7H3/t20-,23+,24-,25-,26-,27+,28-,29-,30+,32+,33+/m0/s1

InChI Key

CEFWIVSCALJZMU-ZZGCFVDSSA-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 axillaris FRANCH	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 16-oxosteroids. These are steroid derivatives carrying a C=O group at the 16-position of the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Oxosteroids

Direct Parent

16-oxosteroids

Alternative Parents

Substituents

22-azasteroid
Pregnane-skeleton
Steroid ester
Steroidal alkaloid
Pregnane-type alkaloid
16-hydroxysteroid
16-beta-hydroxysteroid
16-oxosteroid
Hydroxysteroid
Azasteroid
Alkaloid or derivatives
Benzoic acid or derivatives
Benzamide
Benzoyl
Benzenoid
Monocyclic benzene moiety
Tertiary carboxylic acid amide
Cyclic alcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Carboxylic acid ester
Carboxamide group
Amino acid or derivatives
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Alcohol
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	4.45	ALOGPS
logP	4.38	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	14.87	ChemAxon
pKa (Strongest Basic)	9.77	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	70.08 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	154.34 m³·mol⁻¹	ChemAxon
Polarizability	62.67 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	Yes	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

162922051

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Paxillarine A (NP0066469)

MOL for NP0066469 (Paxillarine A)

3D MOL for NP0066469 (Paxillarine A)

3D SDF for NP0066469 (Paxillarine A)

3D-SDF for NP0066469 (Paxillarine A)

PDB for NP0066469 (Paxillarine A)

3D PDB for NP0066469 (Paxillarine A)

SMILES for NP0066469 (Paxillarine A)

INCHI for NP0066469 (Paxillarine A)

Structure for NP0066469 (Paxillarine A)

3D Structure for NP0066469 (Paxillarine A)