NP-MRD: Showing NP-Card for (-)-Eburnamenine (NP0067321)

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Record Information

Version

2.0

Created at

2022-04-28 11:55:58 UTC

Updated at

2022-04-28 11:55:58 UTC

NP-MRD ID

NP0067321

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Eburnamenine

Description

(-)-Eburnamenine belongs to the class of organic compounds known as eburnan-type alkaloids. These are alkaloids with a structure based on the eburnan skeleton, that arises from rearrangement of the aspidospermidine ring system, involving migration of C-21 from C-7 to C-2, fission of the 2,16-bond, and attachment of C-16 to N-1. (-)-Eburnamenine is found in Amsonia angustifolia and Vinca minor. (-)-Eburnamenine was first documented in 2016 (PMID: 26667775). Based on a literature review very few articles have been published on (-)-eburnamenine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 47  0  0  0  0  0  0  0  0999 V2000
   -3.6895    1.6109   -0.6759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5398    0.7703   -1.1050 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5879    0.4257    0.0484 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1934    1.6974    0.6479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0367    2.1151    0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0921    1.2723    0.3099 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7973    0.1190   -0.2434 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8844   -0.6141   -0.6040 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9656    0.1445   -0.2508 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3264   -0.0506   -0.3582 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1924    0.9312    0.1040 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6720    2.0967    0.6683 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3114    2.2869    0.7734 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4443    1.3200    0.3184 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6740   -1.9467   -1.2157 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3874   -2.6119   -0.8144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5608   -1.8076   -0.1110 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8731   -2.3726   -0.2918 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9508   -1.5597    0.3900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4261   -0.3384    1.0696 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5250   -0.4204   -0.5269 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3486    1.1451    0.0727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3967    2.6563   -0.3689 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3301    1.8085   -1.5977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9591    1.3777   -1.8634 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9071   -0.1287   -1.6298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9930    2.3628    1.0254 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2606    3.0604    1.2331 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6794   -0.9767   -0.8060 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2475    0.7871    0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3920    2.8395    1.0174 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9411    3.2041    1.2171 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5349   -2.5974   -0.9564 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7077   -1.8026   -2.3156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0935   -3.0357   -1.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6212   -3.4985   -0.1614 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9026   -3.4433    0.0065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1028   -2.3649   -1.3767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3705   -2.2198    1.1950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8127   -1.3275   -0.2632 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7448   -0.6980    1.8981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2559    0.2545    1.4732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6047   -0.4710   -1.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  3  2  1  6
  3 20  1  0
 20 19  1  0
 19 18  1  0
 18 17  1  0
 17 16  1  0
 16 15  1  0
 15  8  1  0
  8  7  2  0
  7 21  1  0
  7  6  1  0
  6  5  1  0
  5  4  2  0
  6 14  1  0
 14 13  2  0
 13 12  1  0
 12 11  2  0
 11 10  1  0
 10  9  2  0
 21  3  1  0
  9 14  1  0
  4  3  1  0
 21 17  1  0
  9  8  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  2 25  1  0
  2 26  1  0
 20 41  1  0
 20 42  1  0
 19 39  1  0
 19 40  1  0
 18 37  1  0
 18 38  1  0
 16 35  1  0
 16 36  1  0
 15 33  1  0
 15 34  1  0
 21 43  1  6
  5 28  1  0
  4 27  1  0
 13 32  1  0
 12 31  1  0
 11 30  1  0
 10 29  1  0
M  END


  Mrv1652304282213562D          

 21 25  0  0  1  0            999 V2000
    6.5058    0.7906    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4665   -0.0335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7333   -0.4116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0392    0.0344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0784    0.8585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8117    1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1617    1.2437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7907    0.5068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2434   -0.1829    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8724   -0.9198    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0487   -0.9670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5961   -0.2772    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9671    0.4596    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.5144    1.1494    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8854    1.8863    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7091    1.9334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6908    1.1022    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3198    0.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7724   -0.3244    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2251   -1.0141    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4014   -1.0613    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  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13  8  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  0  0  0  0
 12 20  1  1  0  0  0
 20 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0067321

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@]12CCCN3CCC4=C([C@H]13)N(C=C2)C1=CC=CC=C41

> <INCHI_IDENTIFIER>
InChI=1S/C19H22N2/c1-2-19-9-5-11-20-12-8-15-14-6-3-4-7-16(14)21(13-10-19)17(15)18(19)20/h3-4,6-7,10,13,18H,2,5,8-9,11-12H2,1H3/t18-,19+/m1/s1

> <INCHI_KEY>
VKTOXAGUZWAECL-MOPGFXCFSA-N

> <FORMULA>
C19H22N2

> <MOLECULAR_WEIGHT>
278.399

> <EXACT_MASS>
278.178298716

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
33.172144727099294

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(15S,19S)-15-ethyl-1,11-diazapentacyclo[9.6.2.0^{2,7}.0^{8,18}.0^{15,19}]nonadeca-2,4,6,8(18),16-pentaene

> <ALOGPS_LOGP>
3.96

> <JCHEM_LOGP>
3.833091976666667

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.347970746871259

> <JCHEM_POLAR_SURFACE_AREA>
8.17

> <JCHEM_REFRACTIVITY>
87.4154

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.94e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(15S,19S)-15-ethyl-1,11-diazapentacyclo[9.6.2.0^{2,7}.0^{8,18}.0^{15,19}]nonadeca-2,4,6,8(18),16-pentaene

> <JCHEM_VEBER_RULE>
1

$$$$

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      12.144   1.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.071  -0.063   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.702  -0.768   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.407   0.064   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.480   1.603   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.849   2.308   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.769   2.322   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.076   0.946   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       7.921  -0.341   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       7.228  -1.717   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.691  -1.805   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.846  -0.517   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.539   0.858   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.694   2.146   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       5.386   3.521   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.924   3.609   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.156   2.057   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.464   0.682   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.309  -0.606   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.153  -1.893   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.616  -1.981   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   16                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   19   20                                             
CONECT   13   12    8   14                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15    7                                                       
CONECT   17   14   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   12                                                       
CONECT   20   12   21                                                       
CONECT   21   20                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₂₂N₂

Average Mass

278.3990 Da

Monoisotopic Mass

278.17830 Da

IUPAC Name

(15S,19S)-15-ethyl-1,11-diazapentacyclo[9.6.2.0^{2,7}.0^{8,18}.0^{15,19}]nonadeca-2,4,6,8(18),16-pentaene

Traditional Name

(15S,19S)-15-ethyl-1,11-diazapentacyclo[9.6.2.0^{2,7}.0^{8,18}.0^{15,19}]nonadeca-2,4,6,8(18),16-pentaene

CAS Registry Number

Not Available

SMILES

CC[C@@]12CCCN3CCC4=C([C@H]13)N(C=C2)C1=CC=CC=C41

InChI Identifier

InChI=1S/C19H22N2/c1-2-19-9-5-11-20-12-8-15-14-6-3-4-7-16(14)21(13-10-19)17(15)18(19)20/h3-4,6-7,10,13,18H,2,5,8-9,11-12H2,1H3/t18-,19+/m1/s1

InChI Key

VKTOXAGUZWAECL-MOPGFXCFSA-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
Amsonia angustifolia	Plant	KNApSAcK
Vinca minor	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as eburnan-type alkaloids. These are alkaloids with a structure based on the eburnan skeleton, that arises from rearrangement of the aspidospermidine ring system, involving migration of C-21 from C-7 to C-2, fission of the 2,16-bond, and attachment of C-16 to N-1.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Eburnan-type alkaloids

Sub Class

Not Available

Direct Parent

Eburnan-type alkaloids

Alternative Parents

Substituents

Eburna alkaloid
Indolo[3,2-1de][1,5]naphthyridine
Beta-carboline
Pyridoindole
3-alkylindole
Naphthyridine
Indole
Indole or derivatives
Aralkylamine
Benzenoid
Piperidine
Heteroaromatic compound
Pyrrole
Tertiary aliphatic amine
Tertiary amine
Organoheterocyclic compound
Azacycle
Amine
Hydrocarbon derivative
Organic nitrogen compound
Organonitrogen compound
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	3.96	ALOGPS
logP	3.83	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Basic)	7.35	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	8.17 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	87.42 m³·mol⁻¹	ChemAxon
Polarizability	33.17 Å³	ChemAxon
Number of Rings	5	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

C00025047

Chemspider ID

24679194

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15559073

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liu Q, Chen CJ, Zhang L, Gao K: Two new indole alkaloids from Hunteria zeylanica. J Asian Nat Prod Res. 2016;18(4):349-53. doi: 10.1080/10286020.2015.1092961. Epub 2015 Dec 14. [PubMed:26667775 ]

Showing NP-Card for (-)-Eburnamenine (NP0067321)

MOL for NP0067321 ((-)-Eburnamenine)

3D MOL for NP0067321 ((-)-Eburnamenine)

3D SDF for NP0067321 ((-)-Eburnamenine)

3D-SDF for NP0067321 ((-)-Eburnamenine)

PDB for NP0067321 ((-)-Eburnamenine)

3D PDB for NP0067321 ((-)-Eburnamenine)

SMILES for NP0067321 ((-)-Eburnamenine)

INCHI for NP0067321 ((-)-Eburnamenine)

Structure for NP0067321 ((-)-Eburnamenine)

3D Structure for NP0067321 ((-)-Eburnamenine)