NP-MRD: Showing NP-Card for genicunin B (NP0031073)

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Record Information

Version

2.0

Created at

2021-06-19 22:15:30 UTC

Updated at

2021-06-29 23:59:26 UTC

NP-MRD ID

NP0031073

Secondary Accession Numbers

None

Natural Product Identification

Common Name

genicunin B

Provided By

JEOL Database JEOL Logo

Description

Genicunine B belongs to the class of organic compounds known as aconitane-type diterpenoid alkaloids. These are alkaloid diterpenoids with a structure based on the hexacyclic aconitane skeleton. These compounds have no oxygen functionality at the C7 atom. genicunin B is found in Aconitum geniculatum and Aconitum variegatum. genicunin B was first documented in 2005 (Diaz, J. G., et al.). Based on a literature review very few articles have been published on Genicunine B.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202100153D          

 66 71  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306202100153D          

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M  END
> <DATABASE_ID>
NP0031073

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])[C@]2([H])C([H])([H])[C@]3(O[H])[C@@]1([H])[C@](O[H])(C([H])([H])[C@]2([H])OC([H])([H])[H])[C@@]1([H])C([H])([H])[C@@]2([H])[C@]33[C@]1([H])N(C([H])([H])C([H])([H])[H])C([H])([H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])OC([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H37NO5/c1-5-24-11-20(2)7-6-16(29-4)23-15(20)8-13(19(23)24)21(26)10-14(28-3)12-9-22(23,27)18(21)17(12)25/h12-19,25-27H,5-11H2,1-4H3/t12-,13+,14+,15-,16+,17+,18-,19-,20+,21+,22+,23+/m1/s1

> <INCHI_KEY>
GBBKFXYNDQUOGN-KOWPDBJSSA-N

> <FORMULA>
C23H37NO5

> <MOLECULAR_WEIGHT>
407.551

> <EXACT_MASS>
407.267173295

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
44.57300808743182

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S,3R,4S,5S,6S,8S,9S,10R,13R,16S,17R)-11-ethyl-6,16-dimethoxy-13-methyl-11-azahexacyclo[7.7.2.1^{2,5}.0^{1,10}.0^{3,8}.0^{13,17}]nonadecane-2,4,8-triol

> <ALOGPS_LOGP>
0.76

> <JCHEM_LOGP>
-0.5306748686666674

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
14.200562539683563

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.573745554771648

> <JCHEM_PKA_STRONGEST_BASIC>
9.840148643369552

> <JCHEM_POLAR_SURFACE_AREA>
82.39000000000001

> <JCHEM_REFRACTIVITY>
107.67879999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.60e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3R,4S,5S,6S,8S,9S,10R,13R,16S,17R)-11-ethyl-6,16-dimethoxy-13-methyl-11-azahexacyclo[7.7.2.1^{2,5}.0^{1,10}.0^{3,8}.0^{13,17}]nonadecane-2,4,8-triol

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

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 22 57  1  0
 22 58  1  0
 22 59  1  0
 11 45  1  0
 11 46  1  0
 11 47  1  0
 26 63  1  0
M  END

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  C   UNK     0      -0.986  -2.876  -2.961  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.271  -1.648  -2.407  0.00  0.00           C+0
HETATM    3  N   UNK     0      -0.513  -1.442  -0.971  0.00  0.00           N+0
HETATM    4  C   UNK     0       0.027  -2.530  -0.140  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.027  -2.227   1.388  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.884  -3.221   2.141  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.450  -2.425   1.947  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.484  -1.545   1.280  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.077  -0.072   1.279  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.945   0.639   0.383  0.00  0.00           O+0
HETATM   11  C   UNK     0      -4.238   0.895   0.916  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.578   0.230   0.922  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.426  -0.754   1.626  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.776  -0.513   0.898  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.382   0.185  -0.429  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.152  -0.069  -0.540  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.704   1.702  -0.336  0.00  0.00           C+0
HETATM   18  O   UNK     0       3.141   1.815  -0.270  0.00  0.00           O+0
HETATM   19  C   UNK     0       1.276   2.465  -1.624  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.307   3.657  -1.452  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.958   4.875  -1.870  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.930   5.062  -3.282  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.155   3.899  -0.007  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.129   2.804   0.470  0.00  0.00           C+0
HETATM   25  C   UNK     0      -0.280   1.762   1.255  0.00  0.00           C+0
HETATM   26  O   UNK     0      -0.552   1.992   2.652  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.155   2.257   0.993  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.016   3.775   0.952  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.221   4.390   0.520  0.00  0.00           O+0
HETATM   30  H   UNK     0      -2.054  -2.853  -2.721  0.00  0.00           H+0
HETATM   31  H   UNK     0      -0.561  -3.806  -2.571  0.00  0.00           H+0
HETATM   32  H   UNK     0      -0.888  -2.903  -4.051  0.00  0.00           H+0
HETATM   33  H   UNK     0       0.801  -1.723  -2.624  0.00  0.00           H+0
HETATM   34  H   UNK     0      -0.650  -0.784  -2.966  0.00  0.00           H+0
HETATM   35  H   UNK     0      -0.543  -3.450  -0.324  0.00  0.00           H+0
HETATM   36  H   UNK     0       1.056  -2.755  -0.446  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.899  -3.003   3.215  0.00  0.00           H+0
HETATM   38  H   UNK     0       1.918  -3.200   1.786  0.00  0.00           H+0
HETATM   39  H   UNK     0       0.526  -4.250   2.015  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.760  -3.472   1.838  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.452  -2.216   3.026  0.00  0.00           H+0
HETATM   42  H   UNK     0      -3.434  -1.663   1.816  0.00  0.00           H+0
HETATM   43  H   UNK     0      -2.706  -1.892   0.264  0.00  0.00           H+0
HETATM   44  H   UNK     0      -2.248   0.297   2.299  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.795  -0.034   1.063  0.00  0.00           H+0
HETATM   46  H   UNK     0      -4.165   1.449   1.857  0.00  0.00           H+0
HETATM   47  H   UNK     0      -4.785   1.510   0.196  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.514  -0.554   2.699  0.00  0.00           H+0
HETATM   49  H   UNK     0       2.334  -1.428   0.686  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.458   0.073   1.522  0.00  0.00           H+0
HETATM   51  H   UNK     0       1.947  -0.249  -1.262  0.00  0.00           H+0
HETATM   52  H   UNK     0      -0.644   0.629  -1.221  0.00  0.00           H+0
HETATM   53  H   UNK     0       3.327   2.754  -0.049  0.00  0.00           H+0
HETATM   54  H   UNK     0       2.179   2.806  -2.147  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.812   1.768  -2.333  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.578   3.510  -2.085  0.00  0.00           H+0
HETATM   57  H   UNK     0       1.473   5.982  -3.514  0.00  0.00           H+0
HETATM   58  H   UNK     0       1.414   4.231  -3.802  0.00  0.00           H+0
HETATM   59  H   UNK     0      -0.103   5.172  -3.628  0.00  0.00           H+0
HETATM   60  H   UNK     0      -0.611   4.894   0.064  0.00  0.00           H+0
HETATM   61  H   UNK     0      -1.645   2.393  -0.400  0.00  0.00           H+0
HETATM   62  H   UNK     0      -1.889   3.252   1.123  0.00  0.00           H+0
HETATM   63  H   UNK     0       0.123   1.532   3.180  0.00  0.00           H+0
HETATM   64  H   UNK     0       1.831   2.028   1.825  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.761   4.182   1.938  0.00  0.00           H+0
HETATM   66  H   UNK     0       1.976   5.069  -0.145  0.00  0.00           H+0
CONECT    1    2   30   31   32                                             
CONECT    2    3    1   33   34                                             
CONECT    3    4    2   16                                                  
CONECT    4    5    3   35   36                                             
CONECT    5    7   13    6    4                                             
CONECT    6    5   37   38   39                                             
CONECT    7    5    8   40   41                                             
CONECT    8    9    7   42   43                                             
CONECT    9    8   10   12   44                                             
CONECT   10    9   11                                                       
CONECT   11   10   45   46   47                                             
CONECT   12   16    9   13   25                                             
CONECT   13   14    5   12   48                                             
CONECT   14   13   15   49   50                                             
CONECT   15   14   16   17   51                                             
CONECT   16   12   15    3   52                                             
CONECT   17   19   18   27   15                                             
CONECT   18   17   53                                                       
CONECT   19   17   20   54   55                                             
CONECT   20   23   21   19   56                                             
CONECT   21   20   22                                                       
CONECT   22   21   57   58   59                                             
CONECT   23   28   24   20   60                                             
CONECT   24   23   25   61   62                                             
CONECT   25   24   27   12   26                                             
CONECT   26   25   63                                                       
CONECT   27   17   25   28   64                                             
CONECT   28   23   29   27   65                                             
CONECT   29   28   66                                                       
CONECT   30    1                                                            
CONECT   31    1                                                            
CONECT   32    1                                                            
CONECT   33    2                                                            
CONECT   34    2                                                            
CONECT   35    4                                                            
CONECT   36    4                                                            
CONECT   37    6                                                            
CONECT   38    6                                                            
CONECT   39    6                                                            
CONECT   40    7                                                            
CONECT   41    7                                                            
CONECT   42    8                                                            
CONECT   43    8                                                            
CONECT   44    9                                                            
CONECT   45   11                                                            
CONECT   46   11                                                            
CONECT   47   11                                                            
CONECT   48   13                                                            
CONECT   49   14                                                            
CONECT   50   14                                                            
CONECT   51   15                                                            
CONECT   52   16                                                            
CONECT   53   18                                                            
CONECT   54   19                                                            
CONECT   55   19                                                            
CONECT   56   20                                                            
CONECT   57   22                                                            
CONECT   58   22                                                            
CONECT   59   22                                                            
CONECT   60   23                                                            
CONECT   61   24                                                            
CONECT   62   24                                                            
CONECT   63   26                                                            
CONECT   64   27                                                            
CONECT   65   28                                                            
CONECT   66   29                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  142    0
END

RDKit          3D

66 71  0  0  0  0  0  0  0  0999 V2000
   -0.9862   -2.8761   -2.9607 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4517   -2.2160    3.0258 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7608    4.1818    1.9376 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9758    5.0686   -0.1454 H   0  0  0  0  0  0  0  0  0  0  0  0
 28 23  1  0
 23 24  1  0
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  8  9  1  0
  9 10  1  0
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  6 37  1  0
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  2 33  1  0
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  1 30  1  0
  1 31  1  0
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 11 45  1  0
 11 46  1  0
 11 47  1  0
 26 63  1  0
M  END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₇NO₅

Average Mass

407.5510 Da

Monoisotopic Mass

407.26717 Da

IUPAC Name

(1R,2S,3R,4S,5S,6S,8S,9S,10R,13R,16S,17R)-11-ethyl-6,16-dimethoxy-13-methyl-11-azahexacyclo[7.7.2.1^{2,5}.0^{1,10}.0^{3,8}.0^{13,17}]nonadecane-2,4,8-triol

Traditional Name

(1R,2S,3R,4S,5S,6S,8S,9S,10R,13R,16S,17R)-11-ethyl-6,16-dimethoxy-13-methyl-11-azahexacyclo[7.7.2.1^{2,5}.0^{1,10}.0^{3,8}.0^{13,17}]nonadecane-2,4,8-triol

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])[C@]2([H])C([H])([H])[C@]3(O[H])[C@@]1([H])[C@](O[H])(C([H])([H])[C@]2([H])OC([H])([H])[H])[C@@]1([H])C([H])([H])[C@@]2([H])[C@]33[C@]1([H])N(C([H])([H])C([H])([H])[H])C([H])([H])[C@]2(C([H])([H])[H])C([H])([H])C([H])([H])[C@]3([H])OC([H])([H])[H]

InChI Identifier

InChI=1S/C23H37NO5/c1-5-24-11-20(2)7-6-16(29-4)23-15(20)8-13(19(23)24)21(26)10-14(28-3)12-9-22(23,27)18(21)17(12)25/h12-19,25-27H,5-11H2,1-4H3/t12-,13+,14+,15-,16+,17+,18-,19-,20+,21+,22+,23+/m1/s1

InChI Key

GBBKFXYNDQUOGN-KOWPDBJSSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CDCl₃, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Aconitum geniculatum	LOTUS Database	35616633
Aconitum variegatum	JEOL database	Diaz, J. G., et al, Phytochemistry 66, 837 (2005)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aconitane-type diterpenoid alkaloids. These are alkaloid diterpenoids with a structure based on the hexacyclic aconitane skeleton. These compounds have no oxygen functionality at the C7 atom.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Aconitane-type diterpenoid alkaloids

Alternative Parents

Substituents

Aconitane-type diterpenoid alkaloid
Quinolidine
Alkaloid or derivatives
Azepane
Piperidine
Tertiary alcohol
Cyclic alcohol
Tertiary aliphatic amine
Tertiary amine
Secondary alcohol
Azacycle
Organoheterocyclic compound
Polyol
Ether
Dialkyl ether
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	0.76	ALOGPS
logP	-0.53	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	13.57	ChemAxon
pKa (Strongest Basic)	9.84	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	82.39 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	107.68 m³·mol⁻¹	ChemAxon
Polarizability	44.57 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

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

102007326

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Diaz, J. G., et al. (2005). Diaz, J. G., et al, Phytochemistry 66, 837 (2005) . Phytochem..

Showing NP-Card for genicunin B (NP0031073)

MOL for NP0031073 (genicunin B)

3D MOL for NP0031073 (genicunin B)

3D SDF for NP0031073 (genicunin B)

3D-SDF for NP0031073 (genicunin B)

PDB for NP0031073 (genicunin B)

3D PDB for NP0031073 (genicunin B)

SMILES for NP0031073 (genicunin B)

INCHI for NP0031073 (genicunin B)

Structure for NP0031073 (genicunin B)

3D Structure for NP0031073 (genicunin B)