NP-MRD: Showing NP-Card for (1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate (NP0147928)

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Record Information

Version

2.0

Created at

2022-09-02 03:36:54 UTC

Updated at

2022-09-02 03:36:55 UTC

NP-MRD ID

NP0147928

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate

Description

7-Senecioylheliotridine belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus. (1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate is found in Cynoglossum creticum and Paracaryum intermedium. Based on a literature review very few articles have been published on 7-Senecioylheliotridine.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 37  0  0  0  0  0  0  0  0999 V2000
    5.1278    1.2421    0.3205 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9320    0.5069   -0.1756 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0066   -0.3123   -1.4318 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8076    0.5800    0.4954 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6163   -0.1258    0.0409 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5343   -0.8334   -0.9711 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4553   -0.0075    0.7976 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7321   -0.6564    0.4256 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2683   -1.5562    1.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0198   -0.6180    2.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6935    0.2426    1.4271 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8501   -0.4334    0.8861 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7753   -0.2757   -0.5789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5921    0.2124   -0.9217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1025    0.5216   -2.2833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7672    1.8711   -2.4271 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7992    0.4114    0.3102 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8317    0.5283    0.7592 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6348    1.7481   -0.5330 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8109    2.0478    1.0108 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0387   -0.2424   -1.8422 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7774   -1.3741   -1.2222 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2889    0.1370   -2.1412 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7930    1.1840    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6310   -1.2477   -0.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4682   -2.1142    2.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9624   -2.2783    1.0533 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3927   -0.0784    3.0927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7967   -1.1565    2.9582 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8467   -1.5019    1.1409 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7453    0.0600    1.3249 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6151   -0.5422   -1.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8399    0.2705   -3.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1970   -0.1006   -2.4973 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2007    2.4524   -1.7713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3595    1.4384    0.2949 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  2  0
  5  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
 13 14  2  0
 14 15  1  0
 15 16  1  0
 14 17  1  0
 17  8  1  0
 17 11  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  8 25  1  6
  9 26  1  0
  9 27  1  0
 10 28  1  0
 10 29  1  0
 12 30  1  0
 12 31  1  0
 13 32  1  0
 15 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  6
M  END


  Mrv1652309022205362D          

 17 18  0  0  1  0            999 V2000
   -1.1092   -3.6193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8543   -2.8347    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4063   -2.2216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0473   -2.6631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2076   -1.8785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3444   -1.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9007   -1.8785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
  8 17  1  0  0  0  0
 17 11  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0147928

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CC(=O)O[C@H]1CCN2CC=C(CO)[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C13H19NO3/c1-9(2)7-12(16)17-11-4-6-14-5-3-10(8-15)13(11)14/h3,7,11,13,15H,4-6,8H2,1-2H3/t11-,13+/m0/s1

> <INCHI_KEY>
JWVMHVYNWULPCC-WCQYABFASA-N

> <FORMULA>
C13H19NO3

> <MOLECULAR_WEIGHT>
237.299

> <EXACT_MASS>
237.136493476

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
25.77531414304209

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,7aR)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-yl 3-methylbut-2-enoate

> <ALOGPS_LOGP>
0.61

> <JCHEM_LOGP>
0.8870652513333335

> <ALOGPS_LOGS>
-0.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.10678653296355

> <JCHEM_PKA_STRONGEST_BASIC>
8.184480938252188

> <JCHEM_POLAR_SURFACE_AREA>
49.769999999999996

> <JCHEM_REFRACTIVITY>
66.6782

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,7aR)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-yl 3-methylbut-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.071  -6.756   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.595  -5.291   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.625  -4.147   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.088  -4.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.388  -3.507   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.643  -2.362   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       1.894  -3.186   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       3.834   0.294   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       7.281  -3.507   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14    8   11                                                  
MASTER        0    0    0    0    0    0    0    0   17    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₃H₁₉NO₃

Average Mass

237.2990 Da

Monoisotopic Mass

237.13649 Da

IUPAC Name

(1S,7aR)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-yl 3-methylbut-2-enoate

Traditional Name

(1S,7aR)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1H-pyrrolizin-1-yl 3-methylbut-2-enoate

CAS Registry Number

Not Available

SMILES

CC(C)=CC(=O)O[C@H]1CCN2CC=C(CO)[C@H]12

InChI Identifier

InChI=1S/C13H19NO3/c1-9(2)7-12(16)17-11-4-6-14-5-3-10(8-15)13(11)14/h3,7,11,13,15H,4-6,8H2,1-2H3/t11-,13+/m0/s1

InChI Key

JWVMHVYNWULPCC-WCQYABFASA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Cynoglossum creticum	LOTUS Database	35616633
Microparacaryum intermedium	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkaloids and derivatives. These are naturally occurring chemical compounds that contain mostly basic nitrogen atoms. This group also includes some related compounds with neutral and even weakly acidic properties. Also some synthetic compounds of similar structure are attributed to alkaloids. In addition to carbon, hydrogen and nitrogen, alkaloids may also contain oxygen, sulfur and more rarely other elements such as chlorine, bromine, and phosphorus.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Not Available

Sub Class

Not Available

Direct Parent

Alkaloids and derivatives

Alternative Parents

Substituents

Alkaloid or derivatives
Pyrrolizine
Fatty acid ester
Fatty acyl
N-alkylpyrrolidine
1,3-aminoalcohol
Pyrrolidine
Pyrroline
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Amino acid or derivatives
Carboxylic acid ester
Tertiary amine
Tertiary aliphatic amine
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic nitrogen compound
Amine
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	0.61	ALOGPS
logP	0.89	ChemAxon
logS	-0.85	ALOGPS
pKa (Strongest Acidic)	15.11	ChemAxon
pKa (Strongest Basic)	8.18	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	49.77 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	66.68 m³·mol⁻¹	ChemAxon
Polarizability	25.78 Å³	ChemAxon
Number of Rings	2	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

30772338

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91746480

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate (NP0147928)

MOL for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

3D MOL for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

3D SDF for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

3D-SDF for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

PDB for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

3D PDB for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

SMILES for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

INCHI for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

Structure for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)

3D Structure for NP0147928 ((1s,7ar)-7-(hydroxymethyl)-2,3,5,7a-tetrahydro-1h-pyrrolizin-1-yl 3-methylbut-2-enoate)