NP-MRD: Showing NP-Card for 13-(pyridin-3-yl)tridecan-1-amine (NP0307770)

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Record Information

Version

2.0

Created at

2022-09-11 01:08:20 UTC

Updated at

2022-09-11 01:08:20 UTC

NP-MRD ID

NP0307770

Secondary Accession Numbers

None

Natural Product Identification

Common Name

13-(pyridin-3-yl)tridecan-1-amine

Description

13-(Pyridin-3-yl)tridecan-1-amine belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms. 13-(pyridin-3-yl)tridecan-1-amine is found in Theonella swinhoei. 13-(Pyridin-3-yl)tridecan-1-amine is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 52 52  0  0  0  0  0  0  0  0999 V2000
    6.6168    0.6523   -2.4984 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.7233    0.7250   -1.0348 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3416    0.3841   -0.4924 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3379    0.4296    1.0134 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9841    0.1005    1.5941 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5196   -1.2791    1.2065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1751   -1.6192    1.7811 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0933   -0.6653    1.3241 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1861   -1.1291    1.9758 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3419   -0.2693    1.6218 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5855   -0.2665    0.1498 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7755    0.6026   -0.2300 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9165    0.5204   -1.7495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0943    1.3758   -2.1660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3642    0.9223   -1.5454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7840    1.4269   -0.3118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9523    1.0182    0.2726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7061    0.0855   -0.4014 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3382   -0.4248   -1.5894 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1891   -0.0069   -2.1392 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4138    1.1668   -2.9354 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7263    1.0904   -2.8238 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0605    1.7210   -0.7362 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4149   -0.0670   -0.6697 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1363   -0.6772   -0.8011 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5569    1.0430   -0.8707 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0647   -0.2840    1.4582 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6106    1.4480    1.3477 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0680    0.2072    2.6896 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2270    0.8225    1.1699 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2788   -2.0017    1.5665 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4639   -1.3761    0.1116 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8979   -2.6320    1.4299 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2648   -1.6532    2.8806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2838    0.3775    1.5978 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9674   -0.6949    0.2232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942   -1.1707    3.0839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3775   -2.2013    1.6735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1537    0.7461    2.0351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2682   -0.6333    2.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7417    0.0736   -0.4605 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8149   -1.3038   -0.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6652    0.1848    0.2644 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6310    1.6525    0.0852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1517   -0.5140   -2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0214    0.9135   -2.2366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8924    2.4162   -1.8489 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1763    1.2987   -3.2753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1806    2.1464    0.1851 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2862    1.4009    1.2244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6319   -0.2585    0.0301 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9066   -0.4287   -3.0984 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
  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  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 15  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  0
  2 24  1  0
  3 25  1  0
  3 26  1  0
  4 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  0
  6 32  1  0
  7 33  1  0
  7 34  1  0
  8 35  1  0
  8 36  1  0
  9 37  1  0
  9 38  1  0
 10 39  1  0
 10 40  1  0
 11 41  1  0
 11 42  1  0
 12 43  1  0
 12 44  1  0
 13 45  1  0
 13 46  1  0
 14 47  1  0
 14 48  1  0
 16 49  1  0
 17 50  1  0
 18 51  1  0
 20 52  1  0
M  END


  Mrv1533004231522162D          

 20 20  0  0  0  0            999 V2000
    4.2868   -9.0750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4315   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.1460   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8605   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5749   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039   -8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184   -9.0750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7184   -9.9000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0039  -10.3125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.2894   -9.9000    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
  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  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 15 20  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0307770

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NCCCCCCCCCCCCCC1=CC=CN=C1

> <INCHI_IDENTIFIER>
InChI=1S/C18H32N2/c19-15-11-9-7-5-3-1-2-4-6-8-10-13-18-14-12-16-20-17-18/h12,14,16-17H,1-11,13,15,19H2

> <INCHI_KEY>
FWWOXZZGLJCQAW-UHFFFAOYSA-N

> <FORMULA>
C18H32N2

> <MOLECULAR_WEIGHT>
276.468

> <EXACT_MASS>
276.256549038

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
36.86619842728752

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
13-(pyridin-3-yl)tridecan-1-amine

> <ALOGPS_LOGP>
5.99

> <JCHEM_LOGP>
5.060258344999999

> <ALOGPS_LOGS>
-6.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.205507202243185

> <JCHEM_POLAR_SURFACE_AREA>
38.91

> <JCHEM_REFRACTIVITY>
87.74049999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.56e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
13-(pyridin-3-yl)tridecan-1-amine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  N   UNK     0       8.002 -16.940   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       9.336 -16.170   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.669 -16.940   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.003 -16.170   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.337 -16.940   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.670 -16.170   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      16.004 -16.940   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      17.338 -16.170   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.672 -16.940   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      20.005 -16.170   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      21.339 -16.940   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      22.673 -16.170   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      24.006 -16.940   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      25.340 -16.170   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      26.674 -16.940   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      28.007 -16.170   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      29.341 -16.940   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      29.341 -18.480   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      28.007 -19.250   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      26.674 -18.480   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
MASTER        0    0    0    0    0    0    0    0   20    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₈H₃₂N₂

Average Mass

276.4680 Da

Monoisotopic Mass

276.25655 Da

IUPAC Name

13-(pyridin-3-yl)tridecan-1-amine

Traditional Name

13-(pyridin-3-yl)tridecan-1-amine

CAS Registry Number

Not Available

SMILES

NCCCCCCCCCCCCCC1=CC=CN=C1

InChI Identifier

InChI=1S/C18H32N2/c19-15-11-9-7-5-3-1-2-4-6-8-10-13-18-14-12-16-20-17-18/h12,14,16-17H,1-11,13,15,19H2

InChI Key

FWWOXZZGLJCQAW-UHFFFAOYSA-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
Theonella swinhoei	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Not Available

Direct Parent

Pyridines and derivatives

Alternative Parents

Substituents

Pyridine
Heteroaromatic compound
Azacycle
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Organonitrogen compound
Primary aliphatic amine
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	5.99	ALOGPS
logP	5.06	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Basic)	10.21	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	38.91 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	87.74 m³·mol⁻¹	ChemAxon
Polarizability	36.87 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9970700

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 13-(pyridin-3-yl)tridecan-1-amine (NP0307770)

MOL for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

3D MOL for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

3D SDF for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

3D-SDF for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

PDB for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

3D PDB for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

SMILES for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

INCHI for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

Structure for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)

3D Structure for NP0307770 (13-(pyridin-3-yl)tridecan-1-amine)