NP-MRD: Showing NP-Card for Tabernamine (NP0050907)

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Record Information

Version

2.0

Created at

2022-04-27 22:22:31 UTC

Updated at

2022-04-27 22:22:31 UTC

NP-MRD ID

NP0050907

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Tabernamine

Description

Tabernamine is found in Tabernaemontana johnstonii.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200222D          

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M  END

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M  END


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    5.1775   -0.7049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8884    0.0678    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0747    0.2038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9913   -0.8409    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.2021   -1.6703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9123   -2.1782    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5013   -1.7004    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.1649   -1.3332    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.9600   -0.4845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2700    0.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4586   -0.1277    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0658    0.5977    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6344    1.1955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3786    0.8395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0590    1.3060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9953    2.1285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2511    2.4845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5706    2.0180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6165   -2.0726    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2736   -2.8453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4287   -2.8738    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0416   -3.6599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2741   -4.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4726   -2.1246    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3605   -0.8448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5886   -1.1566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8110   -0.0052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7204   -0.3535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2658    0.2753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4008    0.4423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7068   -0.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9655   -1.2101    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7126   -1.4820    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9149   -0.6775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0632   -0.0024    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1333   -0.5505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2311   -1.3810    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2762   -2.0800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1187   -2.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6643   -0.1036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  2  0  0  0  0
 10  7  1  6  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  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 16 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 19 24  2  0  0  0  0
 14 25  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 12 27  1  1  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 25 30  1  0  0  0  0
 13 31  1  6  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  1  0  0  0  0
  3 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 38 37  1  6  0  0  0
 38 39  1  0  0  0  0
  2 39  1  0  0  0  0
 39 40  1  6  0  0  0
 41 40  1  6  0  0  0
 41 42  1  0  0  0  0
 42 43  1  0  0  0  0
 38 43  1  0  0  0  0
 43 44  1  1  0  0  0
 44 45  1  0  0  0  0
 41 46  1  0  0  0  0
 37 46  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050907

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H]1C[C@@H]2C[C@@H]3[C@H]1N(C2)CCC1=C3NC2=CC(=CC=C12)[C@H]1C[C@H]2[C@@H]([C@@H](CC3=C1NC1=CC=CC=C31)N(C)C\C2=C\C)C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C40H48N4O2/c1-5-23-15-22-16-32-37-28(13-14-44(20-22)39(23)32)27-12-11-25(17-34(27)42-37)30-18-29-24(6-2)21-43(3)35(36(29)40(45)46-4)19-31-26-9-7-8-10-33(26)41-38(30)31/h6-12,17,22-23,29-30,32,35-36,39,41-42H,5,13-16,18-21H2,1-4H3/b24-6-/t22-,23+,29-,30-,32+,35-,36+,39+/m1/s1

> <INCHI_KEY>
MTARGWPMLJBYNG-JVFFMHQMSA-N

> <FORMULA>
C40H48N4O2

> <MOLECULAR_WEIGHT>
616.85

> <EXACT_MASS>
616.377726802

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
94

> <JCHEM_AVERAGE_POLARIZABILITY>
73.13464789545819

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1R,12R,14S,15E,18S)-12-[(1R,15R,17S,18S)-17-ethyl-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2(10),4,6,8-tetraen-6-yl]-15-ethylidene-17-methyl-10,17-diazatetracyclo[12.3.1.0^{3,11}.0^{4,9}]octadeca-3(11),4,6,8-tetraene-18-carboxylate

> <ALOGPS_LOGP>
6.28

> <JCHEM_LOGP>
6.533930437666667

> <ALOGPS_LOGS>
-5.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
16.879470966090462

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.630873427674153

> <JCHEM_PKA_STRONGEST_BASIC>
9.071481816022967

> <JCHEM_POLAR_SURFACE_AREA>
64.36

> <JCHEM_REFRACTIVITY>
186.392

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.88e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1R,12R,14S,15E,18S)-12-[(1R,15R,17S,18S)-17-ethyl-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2(10),4,6,8-tetraen-6-yl]-15-ethylidene-17-methyl-10,17-diazatetracyclo[12.3.1.0^{3,11}.0^{4,9}]octadeca-3(11),4,6,8-tetraene-18-carboxylate

> <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  N   UNK     0       5.962  -3.209   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       4.677  -2.360   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.088  -0.876   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.627  -0.808   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.167  -2.251   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.685  -2.504   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.665  -1.316   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.125   0.127   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.606   0.380   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.184  -1.570   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      11.577  -3.118   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      12.903  -4.066   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.002  -3.174   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.241  -2.489   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.859  -0.904   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      13.571   0.040   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.056  -0.238   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      11.323   1.116   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0      12.384   2.232   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      13.773   1.567   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      15.044   2.438   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.925   3.973   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.535   4.638   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.265   3.767   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0      16.084  -3.869   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0      15.444  -5.311   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      13.867  -5.364   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      13.144  -6.832   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.712  -7.522   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      17.682  -3.966   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.740  -1.577   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      12.299  -2.159   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      14.581  -0.010   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      16.278  -0.660   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.229   0.514   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       2.615   0.826   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       1.319  -0.310   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       1.802  -2.259   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       3.197  -2.766   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       3.574  -1.265   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       1.985  -0.004   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       0.249  -1.028   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       0.431  -2.578   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -0.516  -3.883   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -2.088  -3.995   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       3.107  -0.193   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3   39                                                  
CONECT    3    2    4   35                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    4                                                       
CONECT   10    7   11   17                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   27                                                  
CONECT   13   12   14   31                                                  
CONECT   14   13   15   25                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   10   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   16   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25   14   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   12   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28                                                            
CONECT   30   25                                                            
CONECT   31   13   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33                                                            
CONECT   35    3   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38   46                                                  
CONECT   38   37   39   43                                                  
CONECT   39   38    2   40                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42   46                                                  
CONECT   42   41   43                                                       
CONECT   43   42   38   44                                                  
CONECT   44   43   45                                                       
CONECT   45   44                                                            
CONECT   46   41   37                                                       
MASTER        0    0    0    0    0    0    0    0   46    0  108    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₀H₄₈N₄O₂

Average Mass

616.8500 Da

Monoisotopic Mass

616.37773 Da

IUPAC Name

methyl (1R,12R,14S,15E,18S)-12-[(1R,15R,17S,18S)-17-ethyl-3,13-diazapentacyclo[13.3.1.0^{2,10}.0^{4,9}.0^{13,18}]nonadeca-2(10),4,6,8-tetraen-6-yl]-15-ethylidene-17-methyl-10,17-diazatetracyclo[12.3.1.0^{3,11}.0^{4,9}]octadeca-3(11),4,6,8-tetraene-18-carboxylate

Traditional Name

CAS Registry Number

Not Available

SMILES

CC[C@H]1C[C@@H]2C[C@@H]3[C@H]1N(C2)CCC1=C3NC2=CC(=CC=C12)[C@H]1C[C@H]2[C@@H]([C@@H](CC3=C1NC1=CC=CC=C31)N(C)C\C2=C\C)C(=O)OC

InChI Identifier

InChI=1S/C40H48N4O2/c1-5-23-15-22-16-32-37-28(13-14-44(20-22)39(23)32)27-12-11-25(17-34(27)42-37)30-18-29-24(6-2)21-43(3)35(36(29)40(45)46-4)19-31-26-9-7-8-10-33(26)41-38(30)31/h6-12,17,22-23,29-30,32,35-36,39,41-42H,5,13-16,18-21H2,1-4H3/b24-6-/t22-,23+,29-,30-,32+,35-,36+,39+/m1/s1

InChI Key

MTARGWPMLJBYNG-JVFFMHQMSA-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
Tabernaemontana johnstonii	Plant	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	6.28	ALOGPS
logP	6.53	ChemAxon
logS	-5.8	ALOGPS
pKa (Strongest Acidic)	15.63	ChemAxon
pKa (Strongest Basic)	9.07	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	64.36 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	186.39 m³·mol⁻¹	ChemAxon
Polarizability	73.13 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Tabernamine (NP0050907)

MOL for NP0050907 (Tabernamine)

3D MOL for NP0050907 (Tabernamine)

3D SDF for NP0050907 (Tabernamine)

3D-SDF for NP0050907 (Tabernamine)

PDB for NP0050907 (Tabernamine)

3D PDB for NP0050907 (Tabernamine)

SMILES for NP0050907 (Tabernamine)

INCHI for NP0050907 (Tabernamine)

Structure for NP0050907 (Tabernamine)

3D Structure for NP0050907 (Tabernamine)