NP-MRD: Showing NP-Card for subulacine (NP0038126)

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Record Information

Version

2.0

Created at

2021-06-20 20:53:59 UTC

Updated at

2021-06-30 00:10:44 UTC

NP-MRD ID

NP0038126

Secondary Accession Numbers

None

Natural Product Identification

Common Name

subulacine

Provided By

JEOL Database JEOL Logo

Description

1,2Beta-Epoxytrachelanthamidine belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom. subulacine is found in Heliotropium angiospermum, Heliotropium transalpinum and Heliotropium transalpinum var. transalpinum Vell. subulacine was first documented in 2009 (Medina, J.C.M., et al.). Based on a literature review very few articles have been published on 1,2beta-Epoxytrachelanthamidine.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306202122543D          

 24 26  0  0  0  0            999 V2000
   -3.8071   -3.6795   -2.9172 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7327   -2.9669   -2.3106 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7659   -1.5249   -2.6785 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0776   -0.9777   -2.9320 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1448   -1.0416   -4.0234 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3606    0.1934   -4.3195 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6931    0.5777   -3.0563 N   0  0  1  0  0  0  0  0  0  0  0  0
   -2.4088    1.6638   -2.3720 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0108    1.4709   -0.9223 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.0617   -0.0371   -0.7470 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7344   -0.5907   -2.1294 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5913   -3.1061   -2.8246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7955   -3.4284   -2.6361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8170   -3.0883   -1.2262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3215   -1.7129   -4.8472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9862    0.9894   -4.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5871   -0.0430   -5.0585 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1013    2.6437   -2.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4985    1.5804   -2.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9907    1.8365   -0.7517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6800    1.9905   -0.2304 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0596   -0.3430   -0.4114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3389   -0.3656    0.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7483   -1.0697   -2.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0  0  0  0
  7  8  1  0  0  0  0
  7  6  1  0  0  0  0
  6  5  1  0  0  0  0
  5  3  1  0  0  0  0
  3 11  1  0  0  0  0
 11  7  1  0  0  0  0
 11 24  1  1  0  0  0
  5  4  1  0  0  0  0
  3  4  1  0  0  0  0
 11 10  1  0  0  0  0
  3  2  1  6  0  0  0
 10  9  1  0  0  0  0
  2  1  1  0  0  0  0
 10 22  1  0  0  0  0
 10 23  1  0  0  0  0
  9 20  1  0  0  0  0
  9 21  1  0  0  0  0
  8 18  1  0  0  0  0
  8 19  1  0  0  0  0
  6 16  1  0  0  0  0
  6 17  1  0  0  0  0
  5 15  1  6  0  0  0
  2 13  1  0  0  0  0
  2 14  1  0  0  0  0
  1 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0038126

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]12O[C@@]1([H])C([H])([H])N1C([H])([H])C([H])([H])C([H])([H])[C@@]21[H]

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO2/c10-5-8-6-2-1-3-9(6)4-7(8)11-8/h6-7,10H,1-5H2/t6-,7-,8+/m0/s1

> <INCHI_KEY>
FRPJEHRSJNAWEI-BIIVOSGPSA-N

> <FORMULA>
C8H13NO2

> <MOLECULAR_WEIGHT>
155.197

> <EXACT_MASS>
155.094628663

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.065367670799706

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1aS,6aS,6bS)-hexahydro-1aH-oxireno[2,3-a]pyrrolizin-6b-yl]methanol

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-0.38109055100000017

> <ALOGPS_LOGS>
0.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.234245225880727

> <JCHEM_PKA_STRONGEST_BASIC>
7.962662569625015

> <JCHEM_POLAR_SURFACE_AREA>
36.0

> <JCHEM_REFRACTIVITY>
39.827099999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.07e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1aS,6aS,6bS)-hexahydrooxireno[2,3-a]pyrrolizin-6b-ylmethanol

> <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  O   UNK     0      -3.807  -3.680  -2.917  0.00  0.00           O+0
HETATM    2  C   UNK     0      -2.733  -2.967  -2.311  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.766  -1.525  -2.679  0.00  0.00           C+0
HETATM    4  O   UNK     0      -4.078  -0.978  -2.932  0.00  0.00           O+0
HETATM    5  C   UNK     0      -3.145  -1.042  -4.023  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.361   0.193  -4.319  0.00  0.00           C+0
HETATM    7  N   UNK     0      -1.693   0.578  -3.056  0.00  0.00           N+0
HETATM    8  C   UNK     0      -2.409   1.664  -2.372  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.011   1.471  -0.922  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.062  -0.037  -0.747  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.734  -0.591  -2.129  0.00  0.00           C+0
HETATM   12  H   UNK     0      -4.591  -3.106  -2.825  0.00  0.00           H+0
HETATM   13  H   UNK     0      -1.796  -3.428  -2.636  0.00  0.00           H+0
HETATM   14  H   UNK     0      -2.817  -3.088  -1.226  0.00  0.00           H+0
HETATM   15  H   UNK     0      -3.321  -1.713  -4.847  0.00  0.00           H+0
HETATM   16  H   UNK     0      -2.986   0.989  -4.738  0.00  0.00           H+0
HETATM   17  H   UNK     0      -1.587  -0.043  -5.059  0.00  0.00           H+0
HETATM   18  H   UNK     0      -2.101   2.644  -2.750  0.00  0.00           H+0
HETATM   19  H   UNK     0      -3.498   1.580  -2.469  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.991   1.837  -0.752  0.00  0.00           H+0
HETATM   21  H   UNK     0      -2.680   1.990  -0.230  0.00  0.00           H+0
HETATM   22  H   UNK     0      -3.060  -0.343  -0.411  0.00  0.00           H+0
HETATM   23  H   UNK     0      -1.339  -0.366   0.007  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.748  -1.070  -2.134  0.00  0.00           H+0
CONECT    1    2   12                                                       
CONECT    2    3    1   13   14                                             
CONECT    3    5   11    4    2                                             
CONECT    4    5    3                                                       
CONECT    5    6    3    4   15                                             
CONECT    6    7    5   16   17                                             
CONECT    7    8    6   11                                                  
CONECT    8    9    7   18   19                                             
CONECT    9    8   10   20   21                                             
CONECT   10   11    9   22   23                                             
CONECT   11    3    7   24   10                                             
CONECT   12    1                                                            
CONECT   13    2                                                            
CONECT   14    2                                                            
CONECT   15    5                                                            
CONECT   16    6                                                            
CONECT   17    6                                                            
CONECT   18    8                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21    9                                                            
CONECT   22   10                                                            
CONECT   23   10                                                            
CONECT   24   11                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Value	Source
1,2b-Epoxytrachelanthamidine	Generator
1,2Β-epoxytrachelanthamidine	Generator

Chemical Formula

C₈H₁₃NO₂

Average Mass

155.1970 Da

Monoisotopic Mass

155.09463 Da

IUPAC Name

[(1aS,6aS,6bS)-hexahydro-1aH-oxireno[2,3-a]pyrrolizin-6b-yl]methanol

Traditional Name

(1aS,6aS,6bS)-hexahydrooxireno[2,3-a]pyrrolizin-6b-ylmethanol

CAS Registry Number

Not Available

SMILES

[H]OC([H])([H])[C@]12O[C@@]1([H])C([H])([H])N1C([H])([H])C([H])([H])C([H])([H])[C@@]21[H]

InChI Identifier

InChI=1S/C8H13NO2/c10-5-8-6-2-1-3-9(6)4-7(8)11-8/h6-7,10H,1-5H2/t6-,7-,8+/m0/s1

InChI Key

FRPJEHRSJNAWEI-BIIVOSGPSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
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, 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, 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, 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, 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
Heliotropium angiospermum	LOTUS Database	35616633
Heliotropium transalpinum	LOTUS Database	35616633
Heliotropium transalpinum var. transalpinum Vell	JEOL database	Medina, J.C.M., et al, Tetrahedron Lett. 50, 2640 (2009)

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrrolizidines. Pyrrolizidines are compounds containing a pyrrolizidine, which is a bicyclic ring system made up of two fused pyrrolidine ring sharing a nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrrolizidines

Sub Class

Not Available

Direct Parent

Pyrrolizidines

Alternative Parents

Substituents

Pyrrolizidine
Morpholine
Oxazinane
N-alkylpyrrolidine
1,3-aminoalcohol
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Dialkyl ether
Oxirane
Ether
Oxacycle
Azacycle
Organonitrogen compound
Organic oxygen compound
Alcohol
Organooxygen compound
Hydrocarbon derivative
Primary alcohol
Amine
Organic nitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-0.2	ALOGPS
logP	-0.38	ChemAxon
logS	0.72	ALOGPS
pKa (Strongest Acidic)	14.23	ChemAxon
pKa (Strongest Basic)	7.96	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	36 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	39.83 m³·mol⁻¹	ChemAxon
Polarizability	16.07 Å³	ChemAxon
Number of Rings	3	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

61636215

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14110209

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Medina, J.C.M., et al. (2009). Medina, J.C.M., et al, Tetrahedron Lett. 50, 2640 (2009). Tetrahedron Lett.

Showing NP-Card for subulacine (NP0038126)

MOL for NP0038126 (subulacine)

3D MOL for NP0038126 (subulacine)

3D SDF for NP0038126 (subulacine)

3D-SDF for NP0038126 (subulacine)

PDB for NP0038126 (subulacine)

3D PDB for NP0038126 (subulacine)

SMILES for NP0038126 (subulacine)

INCHI for NP0038126 (subulacine)

Structure for NP0038126 (subulacine)

3D Structure for NP0038126 (subulacine)