NP-MRD: Showing NP-Card for [(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid (NP0214274)

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Record Information

Version

1.0

Created at

2022-09-05 13:31:53 UTC

Updated at

2022-09-05 13:31:53 UTC

NP-MRD ID

NP0214274

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid

Description

Peripentonine C belongs to the class of organic compounds known as n-acyl amines. N-acyl amines are compounds containing a fatty acid moiety linked to an amine group through an ester linkage. [(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid is found in Peripentadenia mearsii. It was first documented in 2007 (PMID: 18039010). Based on a literature review very few articles have been published on peripentonine C.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 48 48  0  0  0  0  0  0  0  0999 V2000
    6.7378   -0.2768   -0.1505 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8615    0.1555   -1.2761 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4086    0.0996   -0.8027 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2020    1.0137    0.3710 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7739    0.9686    0.8831 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4081   -0.3910    1.3335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3129   -0.9666    2.2547 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4259   -1.0792    1.0147 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3125   -0.9081    0.1660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9327   -0.4321    0.9251 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0858   -0.3082   -0.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2545    0.1254    0.6408 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2179    1.4803    1.1141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2637    2.2583    0.3359 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8120    1.2885   -0.6981 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4975   -0.0272   -0.0161 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6769   -1.2125   -0.8829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5304   -2.4690   -0.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5399   -3.5918   -0.7274 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3811   -2.5176    1.2503 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3297    0.5356    0.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1235   -0.7819    0.6283 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4518   -1.0273   -0.5594 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9573   -0.4925   -2.1531 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0713    1.2223   -1.5159 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7758    0.4645   -1.6629 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1496   -0.9441   -0.5634 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9233    0.7655    1.1794 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4487    2.0576    0.0716 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7209    1.6995    1.7395 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1010    1.2992    0.0510 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6188   -1.9067    2.0377 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0927   -1.8585   -0.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5688   -0.1511   -0.6212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6412    0.5912    1.3108 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1187   -1.1240    1.7537 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7712    0.3161   -0.8933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2641   -1.3525   -0.4241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5021    1.5194    2.1706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2452    1.9912    0.9636 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8768    3.1580   -0.1583 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1212    2.5406    0.9794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3629    1.3903   -1.6862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9293    1.3924   -0.7796 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2830   -0.1148    0.8009 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0864   -1.2003   -1.8154 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7567   -1.2002   -1.2197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6254   -1.9992    1.6713 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 20  1  0
 18 19  2  0
 16 12  1  0
  1 21  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  0
  2 25  1  0
  3 26  1  0
  3 27  1  0
  4 28  1  0
  4 29  1  0
  5 30  1  0
  5 31  1  0
  7 32  1  0
  9 33  1  0
  9 34  1  0
 10 35  1  0
 10 36  1  0
 11 37  1  0
 11 38  1  0
 13 39  1  0
 13 40  1  0
 14 41  1  0
 14 42  1  0
 15 43  1  0
 15 44  1  0
 16 45  1  1
 17 46  1  0
 17 47  1  0
 20 48  1  0
M  END


  Mrv1652309052215312D          

 20 20  0  0  1  0            999 V2000
   -3.9565   -3.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2420   -3.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5276   -3.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8131   -3.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0986   -3.9335    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842   -3.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3842   -2.6960    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3303   -3.9335    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -3.5210    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0448   -2.6960    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7593   -2.2835    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7593   -1.4585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0918   -0.9736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3468   -0.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1718   -0.1890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4267   -0.9736    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.2113   -1.2285    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3828   -2.0355    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1675   -2.2904    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7697   -2.5875    0.0000 O   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
  6  8  2  0  0  0  0
  8  9  1  4  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  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0214274

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCC(O)=NCCCN1CCC[C@H]1CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H28N2O3/c1-2-3-4-8-14(18)16-9-6-11-17-10-5-7-13(17)12-15(19)20/h13H,2-12H2,1H3,(H,16,18)(H,19,20)/t13-/m0/s1

> <INCHI_KEY>
BSDQBQJWQLLFQD-ZDUSSCGKSA-N

> <FORMULA>
C15H28N2O3

> <MOLECULAR_WEIGHT>
284.4

> <EXACT_MASS>
284.20999277

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
33.40645710658817

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid

> <JCHEM_LOGP>
-1.2101511054944896

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.60902481272553

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3052623411320003

> <JCHEM_PKA_STRONGEST_BASIC>
10.256299399255383

> <JCHEM_POLAR_SURFACE_AREA>
73.13000000000001

> <JCHEM_REFRACTIVITY>
79.19390000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(2S)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -7.385  -7.343   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.052  -6.573   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.718  -7.343   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.384  -6.573   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.051  -7.343   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.717  -6.573   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -0.717  -5.033   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       0.617  -7.343   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       1.950  -6.573   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.950  -5.033   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.284  -4.263   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       3.284  -2.723   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       2.038  -1.817   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.514  -0.353   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.054  -0.353   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.530  -1.817   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.994  -2.293   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.315  -3.800   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       7.779  -4.275   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       5.170  -4.830   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   12   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₈N₂O₃

Average Mass

284.4000 Da

Monoisotopic Mass

284.20999 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CCCCCC(O)=NCCCN1CCC[C@H]1CC(O)=O

InChI Identifier

InChI=1S/C15H28N2O3/c1-2-3-4-8-14(18)16-9-6-11-17-10-5-7-13(17)12-15(19)20/h13H,2-12H2,1H3,(H,16,18)(H,19,20)/t13-/m0/s1

InChI Key

BSDQBQJWQLLFQD-ZDUSSCGKSA-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
Peripentadenia mearsii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl amines. N-acyl amines are compounds containing a fatty acid moiety linked to an amine group through an ester linkage.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty amides

Direct Parent

N-acyl amines

Alternative Parents

Substituents

N-acyl-amine
N-alkylpyrrolidine
Pyrrolidine
Amino acid or derivatives
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Tertiary amine
Tertiary aliphatic amine
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Azacycle
Organoheterocyclic compound
Organic oxide
Organic nitrogen compound
Amine
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Carbonyl group
Organic oxygen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-1.2	ChemAxon
pKa (Strongest Acidic)	3.31	ChemAxon
pKa (Strongest Basic)	10.26	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

24657896

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24762741

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Katavic PL, Venables DA, Guymer GP, Forster PI, Carroll AR: Alkaloids with human delta-opioid receptor binding affinity from the Australian rainforest tree Peripentadenia mearsii. J Nat Prod. 2007 Dec;70(12):1946-50. doi: 10.1021/np070516x. Epub 2007 Nov 27. [PubMed:18039010 ]
LOTUS database [Link]

Showing NP-Card for [(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid (NP0214274)

MOL for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

3D MOL for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

3D SDF for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

3D-SDF for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

PDB for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

3D PDB for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

SMILES for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

INCHI for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

Structure for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)

3D Structure for NP0214274 ([(2s)-1-{3-[(1-hydroxyhexylidene)amino]propyl}pyrrolidin-2-yl]acetic acid)