NP-MRD: Showing NP-Card for (-)-N-(2-Oxopyrrolidinomethyl)cytisine (NP0068360)

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Record Information

Version

2.0

Created at

2022-04-28 13:31:48 UTC

Updated at

2022-04-28 13:31:48 UTC

NP-MRD ID

NP0068360

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-N-(2-Oxopyrrolidinomethyl)cytisine

Description

(1R,5S)-3-(2-Oxopyrrolizinomethyl)-1,2,3,4,5,6-hexahydro-1,5-methano-8H-pyrido[1,2-a][1,5]diazocine-8-one belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one. (-)-N-(2-Oxopyrrolidinomethyl)cytisine is found in Maackia hupehensis and Malus hupehensis. Based on a literature review very few articles have been published on (1R,5S)-3-(2-Oxopyrrolizinomethyl)-1,2,3,4,5,6-hexahydro-1,5-methano-8H-pyrido[1,2-a][1,5]diazocine-8-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 42 45  0  0  0  0  0  0  0  0999 V2000
   -2.2190   -1.7669   -1.3369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9147   -0.7972   -0.9695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1018   -0.2903   -1.7045 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5917    0.8154   -0.8004 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3074    1.2834   -0.1048 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6885   -0.0100    0.2193 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0280   -0.4145    1.4168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6086   -0.1914    1.4598 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2947    1.1642    1.3361 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8932    1.4623    0.4316 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6206    0.6616   -0.8229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8928   -0.7954   -0.4130 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1914   -1.1593    0.8513 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3674   -0.8460   -0.2969 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1434   -1.8032   -0.9029 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5346   -1.8045   -0.7673 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1356   -0.8235   -0.0093 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3303    0.1163    0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8892    1.0199    1.2803 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9678    0.1012    0.4372 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1831    1.1213    1.0949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8550   -1.1284   -1.6791 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8867    0.0286   -2.7244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2486    0.3996   -0.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0219    1.6022   -1.4204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7377    1.8275   -0.8763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5419    1.8670    0.7922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1769   -1.5015    1.6497 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5553    0.1161    2.2628 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1502    1.7275    0.9191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0889    1.6758    2.3239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8200    2.5486    0.1997 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4017    0.8149   -1.1626 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3868    0.9378   -1.5869 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5334   -1.4101   -1.2662 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9956   -1.4697    1.5838 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4016   -2.0851    0.6940 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6749   -2.5743   -1.4985 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1745   -2.5414   -1.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2264   -0.8157    0.1032 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8054    2.0655    1.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0543    0.8717    2.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
  6  2  1  0
 13  8  1  0
 20 14  1  0
 21 10  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  5 26  1  0
  5 27  1  0
  7 28  1  0
  7 29  1  0
  9 30  1  0
  9 31  1  0
 10 32  1  6
 11 33  1  0
 11 34  1  0
 12 35  1  6
 13 36  1  0
 13 37  1  0
 15 38  1  0
 16 39  1  0
 17 40  1  0
 21 41  1  0
 21 42  1  0
M  END


  Mrv1652304282215312D          

 21 24  0  0  1  0            999 V2000
   -0.0175    0.4109    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0525   -0.4111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6832   -0.9429    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5053   -0.8730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0371   -0.2423    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9671    0.5798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3364    1.1116    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5144    1.0416    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7530    0.1660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6440    1.0514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3909    0.7009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4608   -0.1211    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7839   -0.5927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8539   -1.4147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8037    0.6609    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9803    1.4667    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7361    1.7975    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4479    1.3805    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6551    2.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8492    2.7951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4322    2.0833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  1  8  1  0  0  0  0
  7  9  1  1  0  0  0
  3  9  1  1  0  0  0
  6 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  2  0  0  0  0
  1 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068360

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=C1CCCN1CN1C[C@@H]2C[C@H](C1)C1=CC=CC(=O)N1C2

> <INCHI_IDENTIFIER>
InChI=1S/C16H21N3O2/c20-15-5-2-6-18(15)11-17-8-12-7-13(10-17)14-3-1-4-16(21)19(14)9-12/h1,3-4,12-13H,2,5-11H2/t12-,13+/m0/s1

> <INCHI_KEY>
LKSHQROVPMJSQC-QWHCGFSZSA-N

> <FORMULA>
C16H21N3O2

> <MOLECULAR_WEIGHT>
287.363

> <EXACT_MASS>
287.163376928

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
30.46490951486124

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,9S)-11-[(2-oxopyrrolidin-1-yl)methyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

> <ALOGPS_LOGP>
1.01

> <JCHEM_LOGP>
-0.31416290333333363

> <ALOGPS_LOGS>
-1.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.082221940771124

> <JCHEM_POLAR_SURFACE_AREA>
43.86

> <JCHEM_REFRACTIVITY>
82.21809999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,9S)-11-[(2-oxopyrrolidin-1-yl)methyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

> <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      -0.033   0.767   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       0.098  -0.767   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.275  -1.760   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.810  -1.630   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.802  -0.452   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       3.672   1.082   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.495   2.075   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.960   1.944   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.406   0.310   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.936   1.963   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.330   1.308   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.460  -0.226   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.197  -1.106   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.327  -2.641   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.500   1.234   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -1.830   2.738   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -3.241   3.355   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -4.570   2.577   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -3.089   4.888   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.585   5.218   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.807   3.889   0.000  0.00  0.00           C+0
CONECT    1    2    8   15                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7   10                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    1                                                       
CONECT    9    7    3                                                       
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5   14                                                  
CONECT   14   13                                                            
CONECT   15    1   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   16                                                       
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₂₁N₃O₂

Average Mass

287.3630 Da

Monoisotopic Mass

287.16338 Da

IUPAC Name

(1R,9S)-11-[(2-oxopyrrolidin-1-yl)methyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

Traditional Name

(1R,9S)-11-[(2-oxopyrrolidin-1-yl)methyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one

CAS Registry Number

Not Available

SMILES

O=C1CCCN1CN1C[C@@H]2C[C@H](C1)C1=CC=CC(=O)N1C2

InChI Identifier

InChI=1S/C16H21N3O2/c20-15-5-2-6-18(15)11-17-8-12-7-13(10-17)14-3-1-4-16(21)19(14)9-12/h1,3-4,12-13H,2,5-11H2/t12-,13+/m0/s1

InChI Key

LKSHQROVPMJSQC-QWHCGFSZSA-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
Maackia hupehensis	LOTUS Database	35616633
Malus hupehensis	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cytisine and derivatives. These are lupin alkaloids with a structure based on the cytisine skeleton, which is a tetracyclic ketone containing fused pyridine and piperidine rings that form pyrido[1,2a][1,5]diazocin-8-one.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Lupin alkaloids

Sub Class

Cytisine and derivatives

Direct Parent

Cytisine and derivatives

Alternative Parents

Substituents

Cytisine
Pyridinone
Piperidine
Pyridine
Pyrrolidone
N-alkylpyrrolidine
2-pyrrolidone
Heteroaromatic compound
Pyrrolidine
Tertiary carboxylic acid amide
Carboxamide group
Lactam
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic nitrogen 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	1.01	ALOGPS
logP	-0.31	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Basic)	7.08	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	43.86 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	82.22 m³·mol⁻¹	ChemAxon
Polarizability	30.46 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

8812388

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10637026

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-N-(2-Oxopyrrolidinomethyl)cytisine (NP0068360)

MOL for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

3D MOL for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

3D SDF for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

3D-SDF for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

PDB for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

3D PDB for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

SMILES for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

INCHI for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

Structure for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)

3D Structure for NP0068360 ((-)-N-(2-Oxopyrrolidinomethyl)cytisine)