NP-MRD: Showing NP-Card for Strychnine (NP0000001)

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Record Information

Version

2.0

Created at

2019-05-20 17:30:31 UTC

Updated at

2024-09-03 04:21:43 UTC

NP-MRD ID

NP0000001

Natural Product DOI

https://doi.org/10.57994/2582

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Strychnine

Description

Strychnine, also known as strychnin, is an extremely poisonous and bitter indoline alkaloid. It belongs to the class of organic compounds known as strychnos alkaloids. These are alkaloids having a core structure based on the strychnan, stemmadenine (seco-curan), or the akuammicine (curan) skeleton. Strychnine is also classified as a terpene indole alkaloid belonging to the Strychnos family of Corynanthe alkaloids. In nature, strychnine is most commonly found in the seeds of the Strychnos nux-vomica tree. Strychnine is derived from two smaller, simpler compounds, tryptamine and secologanin. The enzyme, strictosidine synthase, catalyzes the condensation of tryptamine and secologanin, followed by a spontaneous reaction to form strictosidine. Several other enzymatic steps eventually lead to the conversion of strictosidine to strychnine. Strychnine is a colorless, bitter, crystalline alkaloid that is used as a pesticide, particularly for killing small vertebrates such as birds and rodents. Strychnine, when inhaled, swallowed, or absorbed through the eyes or mouth, causes poisoning which results in muscular convulsions and eventually death through asphyxia. Strychnine functions as a neurotoxin which acts as an antagonist of glycine and acetylcholine receptors. It primarily affects the motor nerve fibers in the spinal cord which control muscle contraction. Historically, strychnine has served many purposes: (1) As a medicinal remedy to treat a wide variety of ailments, (2) as an athletic performance enhancer, (3) as a recreational drug, and (4) as a pesticide for killing small vertebrates (PMID: 20810461 ).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652310062121292D          

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M  END

NP0000001
     RDKit          3D

 47 53  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652310062121292D          

 47 53  0  0  1  0            999 V2000
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 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 20 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 36 33  1  1  0  0  0
  7 36  1  0  0  0  0
 36 37  1  0  0  0  0
 29 37  1  0  0  0  0
 37 38  1  6  0  0  0
 37 39  1  0  0  0  0
 39 40  1  0  0  0  0
 39 41  1  0  0  0  0
 39 42  1  0  0  0  0
 25 42  1  0  0  0  0
 42 43  1  6  0  0  0
 42 44  1  0  0  0  0
 17 44  1  0  0  0  0
 44 45  1  6  0  0  0
 44 46  1  0  0  0  0
 11 46  1  0  0  0  0
 36 46  1  0  0  0  0
 46 47  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0000001

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C1=C([H])C([H])=C2C(=C1[H])N1C(=O)C([H])([H])[C@]3([H])OC([H])([H])C([H])=C4C([H])([H])N5C([H])([H])C([H])([H])[C@]22[C@]5([H])C([H])([H])[C@]4([H])[C@]3([H])[C@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C21H22N2O2/c24-18-10-16-19-13-9-17-21(6-7-22(17)11-12(13)5-8-25-16)14-3-1-2-4-15(14)23(18)20(19)21/h1-5,13,16-17,19-20H,6-11H2/t13-,16-,17-,19-,20-,21+/m0/s1

> <INCHI_KEY>
QMGVPVSNSZLJIA-FVWCLLPLSA-N

> <FORMULA>
C21H22N2O2

> <MOLECULAR_WEIGHT>
334.4116

> <EXACT_MASS>
334.168127958

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
35.81142718893862

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,11S,18S,20R,21R,22S)-12-oxa-8,17-diazaheptacyclo[15.5.2.0^{1,18}.0^{2,7}.0^{8,22}.0^{11,21}.0^{15,20}]tetracosa-2,4,6,14-tetraen-9-one

> <ALOGPS_LOGP>
1.68

> <JCHEM_LOGP>
0.9265213356666664

> <ALOGPS_LOGS>
-2.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.23974507177593

> <JCHEM_PKA_STRONGEST_BASIC>
9.27349386578478

> <JCHEM_POLAR_SURFACE_AREA>
32.78

> <JCHEM_REFRACTIVITY>
94.5077

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,11S,18S,20R,21R,22S)-12-oxa-8,17-diazaheptacyclo[15.5.2.0^{1,18}.0^{2,7}.0^{8,22}.0^{11,21}.0^{15,20}]tetracosa-2,4,6,14-tetraen-9-one

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 06-OCT-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-OCT-21         0                                  
HETATM    1  H   UNK     0       0.036  -5.090   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       1.426  -4.425   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.545  -2.890   0.000  0.00  0.00           C+0
HETATM    4  H   UNK     0       0.275  -2.019   0.000  0.00  0.00           H+0
HETATM    5  C   UNK     0       2.935  -2.226   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       3.054  -0.690   0.000  0.00  0.00           H+0
HETATM    7  C   UNK     0       4.204  -3.097   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.085  -4.632   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.696  -5.296   0.000  0.00  0.00           C+0
HETATM   10  H   UNK     0       2.576  -6.832   0.000  0.00  0.00           H+0
HETATM   11  N   UNK     0       5.548  -5.216   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       6.254  -6.622   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.415  -7.914   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.829  -6.694   0.000  0.00  0.00           C+0
HETATM   15  H   UNK     0       7.796  -8.234   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       9.025  -7.664   0.000  0.00  0.00           H+0
HETATM   17  C   UNK     0       8.809  -5.424   0.000  0.00  0.00           C+0
HETATM   18  H   UNK     0       9.509  -4.053   0.000  0.00  0.00           H+0
HETATM   19  O   UNK     0      10.406  -5.342   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.471  -4.112   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0      12.638  -5.117   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0      12.984  -3.824   0.000  0.00  0.00           H+0
HETATM   23  C   UNK     0      11.174  -2.580   0.000  0.00  0.00           C+0
HETATM   24  H   UNK     0      12.467  -1.744   0.000  0.00  0.00           H+0
HETATM   25  C   UNK     0       9.908  -1.690   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.955  -0.111   0.000  0.00  0.00           C+0
HETATM   27  H   UNK     0      10.213   0.776   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       8.984   1.428   0.000  0.00  0.00           H+0
HETATM   29  N   UNK     0       7.250  -0.200   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       5.613   0.053   0.000  0.00  0.00           C+0
HETATM   31  H   UNK     0       5.697   1.590   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       4.408   1.012   0.000  0.00  0.00           H+0
HETATM   33  C   UNK     0       4.759  -1.267   0.000  0.00  0.00           C+0
HETATM   34  H   UNK     0       3.431  -2.047   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       4.479  -2.781   0.000  0.00  0.00           H+0
HETATM   36  C   UNK     0       5.777  -2.539   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       7.140  -1.653   0.000  0.00  0.00           C+0
HETATM   38  H   UNK     0       7.426  -3.166   0.000  0.00  0.00           H+0
HETATM   39  C   UNK     0       8.873  -2.009   0.000  0.00  0.00           C+0
HETATM   40  H   UNK     0       9.461  -0.586   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0       8.151  -0.649   0.000  0.00  0.00           H+0
HETATM   42  C   UNK     0       8.764  -2.977   0.000  0.00  0.00           C+0
HETATM   43  H   UNK     0      10.301  -3.070   0.000  0.00  0.00           H+0
HETATM   44  C   UNK     0       8.017  -4.202   0.000  0.00  0.00           C+0
HETATM   45  H   UNK     0       7.183  -5.497   0.000  0.00  0.00           H+0
HETATM   46  C   UNK     0       6.464  -3.970   0.000  0.00  0.00           C+0
HETATM   47  H   UNK     0       4.931  -3.827   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   36                                                  
CONECT    8    7    9   11                                                  
CONECT    9    8    2   10                                                  
CONECT   10    9                                                            
CONECT   11    8   12   46                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16   17                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   14   18   19   44                                             
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   42                                                  
CONECT   26   25   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26   30   37                                                  
CONECT   30   29   31   32   33                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   30   34   35   36                                             
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   33    7   37   46                                             
CONECT   37   36   29   38   39                                             
CONECT   38   37                                                            
CONECT   39   37   40   41   42                                             
CONECT   40   39                                                            
CONECT   41   39                                                            
CONECT   42   39   25   43   44                                             
CONECT   43   42                                                            
CONECT   44   42   17   45   46                                             
CONECT   45   44                                                            
CONECT   46   44   11   36   47                                             
CONECT   47   46                                                            
MASTER        0    0    0    0    0    0    0    0   47    0  106    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
Strychnin	ChEBI
Strychnidin-10-one	NP-MRD

Chemical Formula

C₂₁H₂₂N₂O₂

Average Mass

334.4116 Da

Monoisotopic Mass

334.16813 Da

IUPAC Name

(1R,11S,18S,20R,21R,22S)-12-oxa-8,17-diazaheptacyclo[15.5.2.0^{1,18}.0^{2,7}.0^{8,22}.0^{11,21}.0^{15,20}]tetracosa-2,4,6,14-tetraen-9-one

Traditional Name

(1R,11S,18S,20R,21R,22S)-12-oxa-8,17-diazaheptacyclo[15.5.2.0^{1,18}.0^{2,7}.0^{8,22}.0^{11,21}.0^{15,20}]tetracosa-2,4,6,14-tetraen-9-one

CAS Registry Number

57-24-9

SMILES

[H]C1=C([H])C([H])=C2C(=C1[H])N1C(=O)C([H])([H])[C@]3([H])OC([H])([H])C([H])=C4C([H])([H])N5C([H])([H])C([H])([H])[C@]22[C@]5([H])C([H])([H])[C@]4([H])[C@]3([H])[C@]12[H]

InChI Identifier

InChI=1S/C21H22N2O2/c24-18-10-16-19-13-9-17-21(6-7-22(17)11-12(13)5-8-25-16)14-3-1-2-4-15(14)23(18)20(19)21/h1-5,13,16-17,19-20H,6-11H2/t13-,16-,17-,19-,20-,21+/m0/s1

InChI Key

QMGVPVSNSZLJIA-FVWCLLPLSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CDCl₃, simulated)	Varshavi.d26			2021-12-06	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	john.cort@pnnl.gov	Not Available	Not Available	2024-05-13	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	john.cort@pnnl.gov	Not Available	Not Available	2024-05-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD3OD, experimental)	john.cort@pnnl.gov	Not Available	Not Available	2024-05-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50.23 MHz, CDCl₃, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CDCl₃, simulated)	v.dorna83@yahoo.com	Not Available	Not Available	2021-08-14	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
nux vomica		Not Available
Strychnos atlantica	KNApSAcK Database	22123792
Strychnos cinnamomifolia	KNApSAcK Database	22123792
Strychnos columbrina	KNApSAcK Database	22123792
Strychnos icaja	LOTUS Database	35616633
Strychnos ignatii	KNApSAcK Database	22123792
Strychnos ligustrina	KNApSAcK Database	22123792
Strychnos lucida	LOTUS Database	35616633
Strychnos lucida R.Br.	KNApSAcK Database	22123792
Strychnos nitida	KNApSAcK Database	22123792
Strychnos nux-vomica	KNApSAcK Database	22123792
Strychnos nux-vomica L.	Seed	7912074
Strychnos panamensis	LOTUS Database	35616633
Strychnos spinosa	KNApSAcK Database	22123792
Strychnos tieute	KNApSAcK Database	22123792
Strychnos triplinervia	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as strychnos alkaloids. These are alkaloids having a core structure based on the strychnan, stemmadenine (seco-curan), or the akuammicine (curan) skeleton.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Strychnos alkaloids

Sub Class

Not Available

Direct Parent

Strychnos alkaloids

Alternative Parents

Substituents

Strychnan skeleton
Akuammicine-skeleton
Stemmadenine-skeleton
Carbazole
Quinolidine
Indole or derivatives
Indolizidine
Aralkylamine
Piperidinone
Delta-lactam
Piperidine
Benzenoid
N-alkylpyrrolidine
Tertiary carboxylic acid amide
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Carboxamide group
Amino acid or derivatives
Lactam
Carboxylic acid derivative
Dialkyl ether
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxide
Amine
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monoterpenoid indole alkaloid (CHEBI:28973 )
Pesticides (C06522 )
Indole alkaloids (C06522 )
Alkaloids (C06522 )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	287.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Boiling Point	284 °C	https://pubchem.ncbi.nlm.nih.gov/compound/Strychnine
Water Solubility	160 mg/L @ 25 °C (exp)	The Good Scents Company Information System
LogP	1.930	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
logP	1.68	ALOGPS
logP	0.93	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	17.24	ChemAxon
pKa (Strongest Basic)	9.27	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	32.78 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	94.51 m³·mol⁻¹	ChemAxon
Polarizability	35.81 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

C00001770

Chemspider ID

389877

KEGG Compound ID

C06522

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Strychnine

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

28973

Good Scents ID

rw1137021

References

General References

Parker AJ, Lee JB, Redman J, Jolliffe L: Strychnine poisoning: gone but not forgotten. Emerg Med J. 2011 Jan;28(1):84. doi: 10.1136/emj.2009.080879. Epub 2010 Sep 1. [PubMed:20810461 ]
Frederich M, De Pauw MC, Llabres G, Tits M, Hayette MP, Brandt V, Penelle J, De Mol P, Angenot L: New antimalarial and cytotoxic sungucine derivatives from Strychnos icaja roots. Planta Med. 2000 Apr;66(3):262-9. doi: 10.1055/s-2000-8559. [PubMed:10821054 ]
Narikawa K, Furue H, Kumamoto E, Yoshimura M: In vivo patch-clamp analysis of IPSCs evoked in rat substantia gelatinosa neurons by cutaneous mechanical stimulation. J Neurophysiol. 2000 Oct;84(4):2171-4. doi: 10.1152/jn.2000.84.4.2171. [PubMed:11024105 ]
Wenstrup J, Leroy SA: Spectral integration in the inferior colliculus: role of glycinergic inhibition in response facilitation. J Neurosci. 2001 Feb 1;21(3):RC124. [PubMed:11157095 ]
Metaxas AE, Cort JR: Counterion influence on chemical shifts in strychnine salts. Magn Reson Chem. 2013 May;51(5):292-8. doi: 10.1002/mrc.3945. Epub 2013 Mar 11. [PubMed:23495106 ]

Showing NP-Card for Strychnine (NP0000001)

MOL for NP0000001 (Strychnine)

3D MOL for NP0000001 (Strychnine)

3D SDF for NP0000001 (Strychnine)

3D-SDF for NP0000001 (Strychnine)

PDB for NP0000001 (Strychnine)

3D PDB for NP0000001 (Strychnine)

SMILES for NP0000001 (Strychnine)

INCHI for NP0000001 (Strychnine)

Structure for NP0000001 (Strychnine)

3D Structure for NP0000001 (Strychnine)