NP-MRD: Showing NP-Card for (2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid (NP0256924)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2022-09-07 21:54:35 UTC

Updated at

2022-09-07 21:54:35 UTC

NP-MRD ID

NP0256924

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid

Description

N-[2-(3-Pyridyl)-ethyl]-L-glutamic acid belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. (2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid is found in Clitocybe acromelalga. Based on a literature review very few articles have been published on N-[2-(3-Pyridyl)-ethyl]-L-glutamic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 34 34  0  0  0  0  0  0  0  0999 V2000
    2.5986    1.7528    1.3860 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6763    1.2555    0.9125 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8660    1.6663    1.4987 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6321    0.2911   -0.2073 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2883   -0.2694   -0.4390 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7073   -1.1836    0.5828 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3777   -1.5179    0.1249 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5533   -0.4669    0.0132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8717   -1.1253   -0.4505 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9473   -0.1447   -0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7666    0.1470    0.4429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7613    1.0760    0.2342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9096    1.6698   -0.9783 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0739    1.3549   -2.0087 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0919    0.4592   -1.8563 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8456   -0.8905    1.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8668   -0.6901    2.7782 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0958   -0.8018    2.6266 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9982    2.6702    1.5761 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3955   -0.5010   -0.0167 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9129    0.8785   -1.1256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5833    0.6101   -0.5914 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2417   -0.7719   -1.4588 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2962   -2.1750    0.4290 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3459   -2.2516   -0.5953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3643    0.3115   -0.7277 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7168    0.0012    1.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7257   -1.6742   -1.3826 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1467   -1.8490    0.3402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6675   -0.3150    1.4262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4322    1.3357    1.0474 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6792    2.4099   -1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4380    0.2198   -2.6818 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4177   -1.4813    3.2792 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  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  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
  6 16  1  0
 16 18  1  0
 16 17  2  0
 15 10  1  0
  3 19  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  6 24  1  1
  7 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
  9 29  1  0
 11 30  1  0
 12 31  1  0
 13 32  1  0
 15 33  1  0
 18 34  1  0
M  END


  Mrv1652309072223542D          

 18 18  0  0  1  0            999 V2000
    2.1434   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.7158   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -6.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  6  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  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 10 15  1  0  0  0  0
  6 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0256924

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC[C@H](NCCC1=CC=CN=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H16N2O4/c15-11(16)4-3-10(12(17)18)14-7-5-9-2-1-6-13-8-9/h1-2,6,8,10,14H,3-5,7H2,(H,15,16)(H,17,18)/t10-/m0/s1

> <INCHI_KEY>
ZFBKXNTVUHWQDE-JTQLQIEISA-N

> <FORMULA>
C12H16N2O4

> <MOLECULAR_WEIGHT>
252.27

> <EXACT_MASS>
252.111007003

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
25.5512967075925

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid

> <JCHEM_LOGP>
-2.5676601878211494

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.23064088631089

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.439802020704171

> <JCHEM_PKA_STRONGEST_BASIC>
10.658617716445152

> <JCHEM_POLAR_SURFACE_AREA>
99.52

> <JCHEM_REFRACTIVITY>
63.273

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0       4.001 -10.010   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      10.669  -9.240   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      12.003 -10.010   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.337  -9.240   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.670 -10.010   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.004  -9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      17.338 -10.010   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.338 -11.550   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      16.004 -12.320   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      14.670 -11.550   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      10.669 -12.320   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       8.002 -12.320   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   16                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16    6   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Value	Source
N-[2-(3-Pyridyl)-ethyl]-L-glutamate	Generator

Chemical Formula

C₁₂H₁₆N₂O₄

Average Mass

252.2700 Da

Monoisotopic Mass

252.11101 Da

IUPAC Name

(2S)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid

Traditional Name

(2S)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC[C@H](NCCC1=CC=CN=C1)C(O)=O

InChI Identifier

InChI=1S/C12H16N2O4/c15-11(16)4-3-10(12(17)18)14-7-5-9-2-1-6-13-8-9/h1-2,6,8,10,14H,3-5,7H2,(H,15,16)(H,17,18)/t10-/m0/s1

InChI Key

ZFBKXNTVUHWQDE-JTQLQIEISA-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
Clitocybe acromelalga	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Glutamic acid and derivatives

Alternative Parents

Substituents

Glutamic acid or derivatives
Alpha-amino acid
L-alpha-amino acid
Amino fatty acid
Aralkylamine
Dicarboxylic acid or derivatives
Pyridine
Fatty acyl
Heteroaromatic compound
Amino acid
Carboxylic acid
Secondary aliphatic amine
Secondary amine
Organoheterocyclic compound
Azacycle
Organonitrogen compound
Organic oxide
Amine
Organic nitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Carbonyl group
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	-2.6	ChemAxon
pKa (Strongest Acidic)	1.44	ChemAxon
pKa (Strongest Basic)	10.66	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	99.52 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	63.27 m³·mol⁻¹	ChemAxon
Polarizability	25.55 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

8259091

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10083553

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid (NP0256924)

MOL for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

3D MOL for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

3D SDF for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

3D-SDF for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

PDB for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

3D PDB for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

SMILES for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

INCHI for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

Structure for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)

3D Structure for NP0256924 ((2s)-2-{[2-(pyridin-3-yl)ethyl]amino}pentanedioic acid)