NP-MRD: Showing NP-Card for Securinine (NP0051379)

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Record Information

Version

2.0

Created at

2022-04-27 22:46:08 UTC

Updated at

2022-04-27 22:46:08 UTC

NP-MRD ID

NP0051379

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Securinine

Description

(1S,2R,8S)-14-oxa-7-azatetracyclo[6.6.1.0¹,¹¹.0²,⁷]Pentadeca-9,11-dien-13-one belongs to the class of organic compounds known as indolizidines. Securinine is found in Breynia coronata, Flueggea suffruticosa, Securinega virosa , Margaritaria discoidea, Margaritaria indica, Phyllanthus amarus, Phyllanthus discoides , Securidaca longepedunculata , Securinega suffruticosa and Securinega suffruticosa var. amamiensis . These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen (1S,2R,8S)-14-oxa-7-azatetracyclo[6.6.1.0¹,¹¹.0²,⁷]Pentadeca-9,11-dien-13-one is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 31 34  0  0  0  0  0  0  0  0999 V2000
    2.7988   -3.0812    1.5350 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3067   -2.0915    0.9580 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9437   -1.3789   -0.1670 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1782   -0.3947   -0.5481 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2277    0.6632   -1.5434 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4238    1.7366   -1.4036 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3796    1.7346   -0.3793 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8678    0.9867    0.8716 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9722   -0.4089    0.3152 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0887   -1.4369    1.2155 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2867   -0.4709   -0.5331 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2637   -1.4366    0.0265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2714   -0.8605    0.9655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9446    0.2813    0.1899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8825    1.2895   -0.0686 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7359    0.8465   -0.7521 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9117   -1.6591   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9084    0.5677   -2.3707 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5798    2.5668   -2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0416    2.7185   -0.0635 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8791    1.3513    1.1353 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1527    1.0719    1.6926 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0494   -0.8864   -1.5284 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7180   -2.2620    0.5494 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8407   -1.9002   -0.8267 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9920   -1.6246    1.2472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7285   -0.4237    1.8243 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7239    0.7485    0.8242 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3551   -0.1321   -0.7452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3538    2.1194   -0.6734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6132    1.7655    0.9049 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  8  1  0
  8  9  1  0
  9 10  1  1
 10  2  1  0
  2  1  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
  6  7  1  0
 16 11  1  0
 16  7  1  0
  4  9  1  0
  7 20  1  1
  8 21  1  0
  8 22  1  0
  3 17  1  0
  5 18  1  0
  6 19  1  0
 11 23  1  6
 12 24  1  0
 12 25  1  0
 13 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 15 30  1  0
 15 31  1  0
M  END


  Mrv1572004221605022D          

 18 21  0  0  1  0            999 V2000
    2.9705    2.4992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4049    1.7977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1459    2.4737    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1796    0.1897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9594   -0.1607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0146    1.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5293    1.5423    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2206    0.9530    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1488    1.0584    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6552    0.3479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7557    1.7468    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2868    2.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8735    1.5714    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1900    1.0454    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7852    2.9924    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5455    2.3544    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2318   -0.2421    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5803    1.7723    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  4  2  0  0  0  0
  6  2  1  0  0  0  0
  9  4  1  0  0  0  0
  9  7  2  0  0  0  0
 10  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  3  1  0  0  0  0
 12  7  1  0  0  0  0
 13  8  1  1  0  0  0
 13  9  1  0  0  0  0
 13 11  1  0  0  0  0
 14  6  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  2  0  0  0  0
 16 12  1  0  0  0  0
 16 13  1  0  0  0  0
 10 17  1  1  0  0  0
 11 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0051379

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]12C[C@@]3(OC(=O)C=C3C=C1)[C@@]1([H])CCCCN21

> <INCHI_IDENTIFIER>
InChI=1S/C13H15NO2/c15-12-7-9-4-5-10-8-13(9,16-12)11-3-1-2-6-14(10)11/h4-5,7,10-11H,1-3,6,8H2/t10-,11-,13+/m1/s1

> <INCHI_KEY>
SWZMSZQQJRKFBP-WZRBSPASSA-N

> <FORMULA>
C13H15NO2

> <MOLECULAR_WEIGHT>
217.268

> <EXACT_MASS>
217.110278727

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
23.080752203433

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,8S)-14-oxa-7-azatetracyclo[6.6.1.0¹,¹¹.0²,⁷]pentadeca-9,11-dien-13-one

> <ALOGPS_LOGP>
1.35

> <JCHEM_LOGP>
1.4055138189999998

> <ALOGPS_LOGS>
-0.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.504628886284037

> <JCHEM_POLAR_SURFACE_AREA>
29.540000000000003

> <JCHEM_REFRACTIVITY>
61.319100000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(-)-securinine

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 22-APR-16   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-16         0                                  
HETATM    1  C   UNK     0       5.545   4.665   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.356   3.356   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.006   4.618   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.335   0.354   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.791  -0.300   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.627   1.999   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.988   2.879   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.278   1.779   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.278   1.976   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.090   0.649   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.277   3.261   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.535   4.359   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.630   2.933   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.088   1.951   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      -1.466   5.586   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       1.018   4.395   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       4.166  -0.452   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       4.817   3.308   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1   11                                                       
CONECT    4    5    9                                                       
CONECT    5    4   10                                                       
CONECT    6    2   14                                                       
CONECT    7    9   12                                                       
CONECT    8   10   13                                                       
CONECT    9    4    7   13                                                  
CONECT   10    5    8   14   17                                             
CONECT   11    3   13   14   18                                             
CONECT   12    7   15   16                                                  
CONECT   13    8    9   11   16                                             
CONECT   14    6   10   11                                                  
CONECT   15   12                                                            
CONECT   16   12   13                                                       
CONECT   17   10                                                            
CONECT   18   11                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

View in JSmol

Synonyms

Value	Source
Allonorsecurinine	MeSH
Allosecurinine	MeSH
Securinan-11-one	MeSH
Securinine	MeSH
Securinine methiodide	MeSH
Securinine nitrate	MeSH

Chemical Formula

C₁₃H₁₅NO₂

Average Mass

217.2680 Da

Monoisotopic Mass

217.11028 Da

IUPAC Name

(1S,2R,8S)-14-oxa-7-azatetracyclo[6.6.1.0¹,¹¹.0²,⁷]pentadeca-9,11-dien-13-one

Traditional Name

(-)-securinine

CAS Registry Number

Not Available

SMILES

[H][C@]12C[C@@]3(OC(=O)C=C3C=C1)[C@@]1([H])CCCCN21

InChI Identifier

InChI=1S/C13H15NO2/c15-12-7-9-4-5-10-8-13(9,16-12)11-3-1-2-6-14(10)11/h4-5,7,10-11H,1-3,6,8H2/t10-,11-,13+/m1/s1

InChI Key

SWZMSZQQJRKFBP-WZRBSPASSA-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
Breynia coronata	Plant	KNApSAcK
Flueggea suffruticosa	LOTUS Database	35616633
Flueggea virosa	Plant	KNApSAcK
Margaritaria discoidea	LOTUS Database	35616633
Margaritaria indica	LOTUS Database	35616633
Phyllanthus amarus	LOTUS Database	35616633
Phyllanthus discoides	Plant	KNApSAcK
Securidaca longipedunculata	Plant	KNApSAcK
Securinega suffruticosa	Plant	KNApSAcK
Securinega suffruticosa var. amamiensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indolizidines. These are polycyclic compounds containing an indolizidine, which is a bicyclic heterocycle containing a saturated six-member ring fused to a saturated five-member ring, one of the bridging atoms being nitrogen.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indolizidines

Sub Class

Not Available

Direct Parent

Indolizidines

Alternative Parents

Substituents

Indolizidine
Azepine
2-furanone
Piperidine
N-alkylpyrrolidine
Dihydrofuran
Pyrrolidine
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Amino acid or derivatives
Carboxylic acid ester
Lactone
Tertiary amine
Tertiary aliphatic amine
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Oxacycle
Azacycle
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Amine
Carbonyl group
Hydrocarbon derivative
Organic nitrogen compound
Organic oxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

indolizines (CHEBI:9079 )

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	1.35	ALOGPS
logP	1.41	ChemAxon
logS	-0.74	ALOGPS
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	29.54 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	61.32 m³·mol⁻¹	ChemAxon
Polarizability	23.08 Å³	ChemAxon
Number of Rings	4	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

C00002360

Chemspider ID

Not Available

KEGG Compound ID

C10614

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442872

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Securinine (NP0051379)

MOL for NP0051379 (Securinine)

3D MOL for NP0051379 (Securinine)

3D SDF for NP0051379 (Securinine)

3D-SDF for NP0051379 (Securinine)

PDB for NP0051379 (Securinine)

3D PDB for NP0051379 (Securinine)

SMILES for NP0051379 (Securinine)

INCHI for NP0051379 (Securinine)

Structure for NP0051379 (Securinine)

3D Structure for NP0051379 (Securinine)