NP-MRD: Showing NP-Card for kopsanone (NP0200619)

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Record Information

Version

2.0

Created at

2022-09-04 19:30:07 UTC

Updated at

2022-09-04 19:30:08 UTC

NP-MRD ID

NP0200619

Secondary Accession Numbers

None

Natural Product Identification

Common Name

kopsanone

Description

Kopsanone belongs to the class of organic compounds known as aspidofractine alkaloids. These are alkaloids with a structure that is based on the hexacyclic aspidofractine core. These compounds are related to the Aspidosperma group by formation of a C-2 to C-18 bond. Kopsanone is an alkaloid isolated from Aspidosperma. kopsanone is found in Kopsia fruticosa and Kopsia officinalis. Kopsanone is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 45 51  0  0  0  0  0  0  0  0999 V2000
   -0.2323    0.8738   -3.6197 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0940    0.6383   -2.4366 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3091    1.7048   -1.3895 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6675    1.3755   -0.7660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5095    0.6924    0.5606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8258    0.2983    1.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4398   -0.8692    0.4257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4898   -1.9946    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1741   -1.6398   -0.1617 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8451   -1.5694   -1.5564 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2792   -0.5999   -1.7294 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5774   -0.1702   -0.3211 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8698   -0.5908    0.1809 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3374   -1.7116    0.8743 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6443   -1.8709    1.2386 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5488   -0.8819    0.9089 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1105    0.2317    0.2257 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7758    0.3979   -0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0880    1.4542   -0.8527 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7293    1.3536   -0.3870 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5365    1.9777    0.9562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8304    1.6961    1.4948 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6097   -0.5195    0.5047 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2634    2.7100   -1.7999 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1263    2.3837   -0.5475 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2977    0.8089   -1.4813 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5238    1.1702    1.0136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7514    0.1251    2.2221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2456   -1.2630    1.1023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9809   -0.5673   -0.5063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9326   -2.5998   -0.6829 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4856   -2.6911    1.0366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7029   -1.3957   -2.2199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4404   -2.5865   -1.8380 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1913   -1.0664   -2.1810 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6340   -2.4733    1.1267 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0163   -2.7242    1.7699 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5948   -0.9481    1.1680 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8352    0.9947   -0.0231 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5313    2.1087   -1.5324 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7689    3.0473    0.8787 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2892    1.5079    1.6490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8186    1.3225    2.5378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4028    2.6468    1.4900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3589   -0.7868    1.5484 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2 11  1  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  5  6  1  1
  5 22  1  0
 22 21  1  0
 21 20  1  0
 20 19  1  6
 19 18  1  0
 18 17  2  0
 17 16  1  0
 16 15  2  0
 15 14  1  0
 14 13  2  0
 12 13  1  1
 12 23  1  0
 20  3  1  0
  3  4  1  0
  3  2  1  0
 12 11  1  0
 23  9  1  0
 23  5  1  0
  4  5  1  0
 12 20  1  0
 13 18  1  0
 11 35  1  6
 10 33  1  0
 10 34  1  0
  8 31  1  0
  8 32  1  0
  7 29  1  0
  7 30  1  0
  6 27  1  0
  6 28  1  0
 22 43  1  0
 22 44  1  0
 21 41  1  0
 21 42  1  0
 19 40  1  0
 17 39  1  0
 16 38  1  0
 15 37  1  0
 14 36  1  0
 23 45  1  1
  3 24  1  6
  4 25  1  0
  4 26  1  0
M  END


  Mrv1533004231514262D          

 23 29  0  0  0  0            999 V2000
    3.0340   -1.4778    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2070   -0.6711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0508    0.1456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1499    0.0855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9999    0.9263    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3966    1.5400    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7881    2.2742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6398    2.3606    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2760    1.8042    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1266    1.8543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3481    1.0183    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5321    0.1525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3847    0.0241    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6041    0.8368    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2832    1.3051    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2172    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4720    2.4815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7928    2.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8589    1.1907    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8428    0.7132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9094    1.0493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7021    0.0346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4305    0.9472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 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
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 14 19  1  0  0  0  0
 19 20  1  0  0  0  0
  3 20  1  0  0  0  0
 12 20  1  0  0  0  0
 20 21  1  0  0  0  0
  5 21  1  0  0  0  0
  9 21  1  0  0  0  0
 12 22  1  0  0  0  0
  2 22  1  0  0  0  0
 22 23  1  0  0  0  0
  9 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0200619

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1C2CN3CCCC45CCC6(NC7=CC=CC=C7C26C34)C1C5

> <INCHI_IDENTIFIER>
InChI=1S/C20H22N2O/c23-16-13-10-18-6-3-9-22-11-14(16)20(17(18)22)12-4-1-2-5-15(12)21-19(13,20)8-7-18/h1-2,4-5,13-14,17,21H,3,6-11H2

> <INCHI_KEY>
RFDVSXYPLPEIGZ-UHFFFAOYSA-N

> <FORMULA>
C20H22N2O

> <MOLECULAR_WEIGHT>
306.409

> <EXACT_MASS>
306.173213336

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
33.582150092744186

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
10,16-diazaheptacyclo[9.8.2.1¹,¹².0²,¹⁶.0³,¹¹.0³,¹⁴.0⁴,⁹]docosa-4,6,8-trien-13-one

> <ALOGPS_LOGP>
2.98

> <JCHEM_LOGP>
2.07231803

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.896768976280583

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.57343609679769

> <JCHEM_PKA_STRONGEST_BASIC>
9.726199676309811

> <JCHEM_POLAR_SURFACE_AREA>
32.34

> <JCHEM_REFRACTIVITY>
89.26069999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
10,16-diazaheptacyclo[9.8.2.1¹,¹².0²,¹⁶.0³,¹¹.0³,¹⁴.0⁴,⁹]docosa-4,6,8-trien-13-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  O   UNK     0       5.663  -2.758   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.986  -1.253   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.695   0.272   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.013   0.160   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.733   1.729   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.607   2.875   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.338   4.245   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.928   4.406   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.115   3.368   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.703   3.461   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.116   1.901   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.460   0.285   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      10.051   0.045   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      10.461   1.562   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      11.729   2.436   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.605   3.971   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.214   4.632   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.947   3.758   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.070   2.223   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.173   1.331   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.431   1.959   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.911   0.065   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.404   1.768   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   22                                                  
CONECT    3    2    4   20                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   21   23                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   20   22                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   14   20                                                  
CONECT   20   19    3   12   21                                             
CONECT   21   20    5    9                                                  
CONECT   22   12    2   23                                                  
CONECT   23   22    9                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₂N₂O

Average Mass

306.4090 Da

Monoisotopic Mass

306.17321 Da

IUPAC Name

10,16-diazaheptacyclo[9.8.2.1¹,¹².0²,¹⁶.0³,¹¹.0³,¹⁴.0⁴,⁹]docosa-4,6,8-trien-13-one

Traditional Name

10,16-diazaheptacyclo[9.8.2.1¹,¹².0²,¹⁶.0³,¹¹.0³,¹⁴.0⁴,⁹]docosa-4,6,8-trien-13-one

CAS Registry Number

Not Available

SMILES

O=C1C2CN3CCCC45CCC6(NC7=CC=CC=C7C26C34)C1C5

InChI Identifier

InChI=1S/C20H22N2O/c23-16-13-10-18-6-3-9-22-11-14(16)20(17(18)22)12-4-1-2-5-15(12)21-19(13,20)8-7-18/h1-2,4-5,13-14,17,21H,3,6-11H2

InChI Key

RFDVSXYPLPEIGZ-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
Kopsia fruticosa	LOTUS Database	35616633
Kopsia officinalis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aspidofractine alkaloids. These are alkaloids with a structure that is based on the hexacyclic aspidofractine core. These compounds are related to the Aspidosperma group by formation of a C-2 to C-18 bond.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Aspidofractine alkaloids

Sub Class

Not Available

Direct Parent

Aspidofractine alkaloids

Alternative Parents

Substituents

Aspidofractine skeleton
Aspidosperma alkaloid
Carbazole
2,3-cyclopentanoindoline
Azaspirodecane
Quinolidine
Indole or derivatives
Dihydroindole
Indolizidine
Aralkylamine
Secondary aliphatic/aromatic amine
Benzenoid
N-alkylpyrrolidine
Piperidine
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Ketone
Organoheterocyclic compound
Secondary amine
Azacycle
Hydrocarbon derivative
Organonitrogen compound
Organic nitrogen compound
Amine
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organooxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic 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	2.98	ALOGPS
logP	2.07	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	16.57	ChemAxon
pKa (Strongest Basic)	9.73	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	32.34 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	89.26 m³·mol⁻¹	ChemAxon
Polarizability	33.58 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Kopsanone

METLIN ID

Not Available

PubChem Compound

433961

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for kopsanone (NP0200619)

MOL for NP0200619 (kopsanone)

3D MOL for NP0200619 (kopsanone)

3D SDF for NP0200619 (kopsanone)

3D-SDF for NP0200619 (kopsanone)

PDB for NP0200619 (kopsanone)

3D PDB for NP0200619 (kopsanone)

SMILES for NP0200619 (kopsanone)

INCHI for NP0200619 (kopsanone)

Structure for NP0200619 (kopsanone)

3D Structure for NP0200619 (kopsanone)