NP-MRD: Showing NP-Card for pyrrolizidine (NP0038610)

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Record Information

Version

2.0

Created at

2021-06-20 21:15:20 UTC

Updated at

2021-06-30 00:11:29 UTC

NP-MRD ID

NP0038610

Secondary Accession Numbers

None

Natural Product Identification

Common Name

pyrrolizidine

Provided By

JEOL Database JEOL Logo

Description

pyrrolizidine is found in Stelletta sp. pyrrolizidine was first documented in 2008 (El-Naggar, M., et al.).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202123153D          

 28 29  0  0  0  0            999 V2000
    1.7207   -2.2842   -4.0559 N   0  3  0  0  0  4  0  0  0  0  0  0
    1.7256   -1.7588   -2.6659 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4542   -0.2515   -2.6316 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0560    0.1575   -3.0935 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0731    1.5892   -2.5906 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6071    1.5472   -1.2437 N   0  3  2  0  0  4  0  0  0  0  0  0
    1.4543    2.7618   -0.9071 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8669    2.3008   -1.2059 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8642    0.8471   -0.7601 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5067    0.3134   -1.1978 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8097   -2.2087   -4.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9470   -3.2935   -4.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4284   -1.8456   -4.6650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7120   -1.9908   -2.2526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9665   -2.3239   -2.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1968    0.2565   -3.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0615    0.1001   -4.1797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110   -0.4772   -2.6331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4731    2.2861   -3.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1065    1.9160   -2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1220    1.4787   -0.5148 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3087    2.9544    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1236    3.6226   -1.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0741    2.3727   -2.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6157    2.8962   -0.6759 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9424    0.7995    0.3331 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7023    0.2811   -1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0703   -0.3743   -0.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10  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 10  1  0  0  0  0
  3  2  1  0  0  0  0
  2  1  1  0  0  0  0
  7 22  1  0  0  0  0
  7 23  1  0  0  0  0
  8 24  1  0  0  0  0
  8 25  1  0  0  0  0
  9 26  1  0  0  0  0
  9 27  1  0  0  0  0
  6 21  1  0  0  0  0
 10 28  1  0  0  0  0
  3 16  1  0  0  0  0
  4 17  1  0  0  0  0
  4 18  1  0  0  0  0
  5 19  1  0  0  0  0
  5 20  1  0  0  0  0
  2 14  1  0  0  0  0
  2 15  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  CHG  2   1   1   6   1
M  END


  Mrv1652306202123153D          

 28 29  0  0  0  0            999 V2000
    1.7207   -2.2842   -4.0559 N   0  3  0  0  0  4  0  0  0  0  0  0
    1.7256   -1.7588   -2.6659 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4542   -0.2515   -2.6316 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0560    0.1575   -3.0935 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0731    1.5892   -2.5906 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6071    1.5472   -1.2437 N   0  3  2  0  0  4  0  0  0  0  0  0
    1.4543    2.7618   -0.9071 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8669    2.3008   -1.2059 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8642    0.8471   -0.7601 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5067    0.3134   -1.1978 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8097   -2.2087   -4.5321 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9470   -3.2935   -4.0611 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4284   -1.8456   -4.6650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7120   -1.9908   -2.2526 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9665   -2.3239   -2.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1968    0.2565   -3.2624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0615    0.1001   -4.1797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110   -0.4772   -2.6331 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4731    2.2861   -3.2348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1065    1.9160   -2.4500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1220    1.4787   -0.5148 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3087    2.9544    0.1610 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1236    3.6226   -1.4942 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0741    2.3727   -2.2799 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6157    2.8962   -0.6759 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9424    0.7995    0.3331 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7023    0.2811   -1.1774 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0703   -0.3743   -0.4645 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10  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 10  1  0  0  0  0
  3  2  1  0  0  0  0
  2  1  1  0  0  0  0
  7 22  1  0  0  0  0
  7 23  1  0  0  0  0
  8 24  1  0  0  0  0
  8 25  1  0  0  0  0
  9 26  1  0  0  0  0
  9 27  1  0  0  0  0
  6 21  1  0  0  0  0
 10 28  1  0  0  0  0
  3 16  1  0  0  0  0
  4 17  1  0  0  0  0
  4 18  1  0  0  0  0
  5 19  1  0  0  0  0
  5 20  1  0  0  0  0
  2 14  1  0  0  0  0
  2 15  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
M  CHG  2   1   1   6   1
M  END
> <DATABASE_ID>
NP0038610

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][N+]([H])([H])C([H])([H])[C@@]1([H])C([H])([H])C([H])([H])[N@+]2([H])C([H])([H])C([H])([H])C([H])([H])[C@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C8H16N2/c9-6-7-3-5-10-4-1-2-8(7)10/h7-8H,1-6,9H2/p+2/t7-,8-/m1/s1

> <INCHI_KEY>
QQRBHSRNSWYCKJ-HTQZYQBOSA-P

> <FORMULA>
C8H18N2

> <MOLECULAR_WEIGHT>
142.245

> <EXACT_MASS>
142.145901428

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
17.372286337862498

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4S,7aR)-1-(azaniumylmethyl)-octahydropyrrolizin-4-ium

> <ALOGPS_LOGP>
-3.00

> <JCHEM_LOGP>
-0.07549939099999992

> <ALOGPS_LOGS>
-4.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_BASIC>
10.803258056708557

> <JCHEM_POLAR_SURFACE_AREA>
32.08

> <JCHEM_REFRACTIVITY>
65.00900000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.84e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,7aR)-1-(ammoniomethyl)-octahydropyrrolizin-4-ium

> <JCHEM_VEBER_RULE>
1

$$$$

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  N   UNK     0       1.721  -2.284  -4.056  0.00  0.00           N+1
HETATM    2  C   UNK     0       1.726  -1.759  -2.666  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.454  -0.252  -2.632  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.056   0.158  -3.094  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.073   1.589  -2.591  0.00  0.00           C+0
HETATM    6  N   UNK     0       0.607   1.547  -1.244  0.00  0.00           N+1
HETATM    7  C   UNK     0       1.454   2.762  -0.907  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.867   2.301  -1.206  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.864   0.847  -0.760  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.507   0.313  -1.198  0.00  0.00           C+0
HETATM   11  H   UNK     0       0.810  -2.209  -4.532  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.947  -3.293  -4.061  0.00  0.00           H+0
HETATM   13  H   UNK     0       2.428  -1.846  -4.665  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.712  -1.991  -2.253  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.967  -2.324  -2.116  0.00  0.00           H+0
HETATM   16  H   UNK     0       2.197   0.257  -3.262  0.00  0.00           H+0
HETATM   17  H   UNK     0      -0.062   0.100  -4.180  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.711  -0.477  -2.633  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.473   2.286  -3.235  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.107   1.916  -2.450  0.00  0.00           H+0
HETATM   21  H   UNK     0      -0.122   1.479  -0.515  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.309   2.954   0.161  0.00  0.00           H+0
HETATM   23  H   UNK     0       1.124   3.623  -1.494  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.074   2.373  -2.280  0.00  0.00           H+0
HETATM   25  H   UNK     0       3.616   2.896  -0.676  0.00  0.00           H+0
HETATM   26  H   UNK     0       2.942   0.800   0.333  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.702   0.281  -1.177  0.00  0.00           H+0
HETATM   28  H   UNK     0       1.070  -0.374  -0.465  0.00  0.00           H+0
CONECT    1    2   11   12   13                                             
CONECT    2    3    1   14   15                                             
CONECT    3   10    4    2   16                                             
CONECT    4    3    5   17   18                                             
CONECT    5    4    6   19   20                                             
CONECT    6    7    5   10   21                                             
CONECT    7    6    8   22   23                                             
CONECT    8    7    9   24   25                                             
CONECT    9    8   10   26   27                                             
CONECT   10    9    3    6   28                                             
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13    1                                                            
CONECT   14    2                                                            
CONECT   15    2                                                            
CONECT   16    3                                                            
CONECT   17    4                                                            
CONECT   18    4                                                            
CONECT   19    5                                                            
CONECT   20    5                                                            
CONECT   21    6                                                            
CONECT   22    7                                                            
CONECT   23    7                                                            
CONECT   24    8                                                            
CONECT   25    8                                                            
CONECT   26    9                                                            
CONECT   27    9                                                            
CONECT   28   10                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₈H₁₈N₂

Average Mass

142.2450 Da

Monoisotopic Mass

142.14590 Da

IUPAC Name

(1R,4S,7aR)-1-(azaniumylmethyl)-octahydropyrrolizin-4-ium

Traditional Name

(1R,4S,7aR)-1-(ammoniomethyl)-octahydropyrrolizin-4-ium

CAS Registry Number

Not Available

SMILES

[H][N+]([H])([H])C([H])([H])[C@@]1([H])C([H])([H])C([H])([H])[N@+]2([H])C([H])([H])C([H])([H])C([H])([H])[C@]12[H]

InChI Identifier

InChI=1S/C8H16N2/c9-6-7-3-5-10-4-1-2-8(7)10/h7-8H,1-6,9H2/p+2/t7-,8-/m1/s1

InChI Key

QQRBHSRNSWYCKJ-HTQZYQBOSA-P

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, CD₃OD, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, CD₃OD, 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
Stelletta sp.	JEOL database	El-Naggar, M., et al, Org. Lett. 10, 4247 (2008)

Chemical Taxonomy

Classification

Not classified

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	ALOGPS
logP	-0.075	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Basic)	10.8	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	32.08 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	65.01 m³·mol⁻¹	ChemAxon
Polarizability	17.37 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

El-Naggar, M., et al. (2008). El-Naggar, M., et al, Org. Lett. 10, 4247 (2008). Org. Lett..

Showing NP-Card for pyrrolizidine (NP0038610)

MOL for NP0038610 (pyrrolizidine)

3D MOL for NP0038610 (pyrrolizidine)

3D SDF for NP0038610 (pyrrolizidine)

3D-SDF for NP0038610 (pyrrolizidine)

PDB for NP0038610 (pyrrolizidine)

3D PDB for NP0038610 (pyrrolizidine)

SMILES for NP0038610 (pyrrolizidine)

INCHI for NP0038610 (pyrrolizidine)

Structure for NP0038610 (pyrrolizidine)

3D Structure for NP0038610 (pyrrolizidine)