NP-MRD: Showing NP-Card for 5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid (NP0253843)

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Record Information

Version

2.0

Created at

2022-09-07 17:50:00 UTC

Updated at

2022-09-07 17:50:00 UTC

NP-MRD ID

NP0253843

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid

Description

5-[5-Carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid belongs to the class of organic compounds known as kainoids. These are non-proteigenous amino acids with a structure characterized by the presence of a pyrrolidine ring bearing two dicarboxylic acid groups. 5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid is found in Clitocybe acromelalga. 5-[5-Carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 36  0  0  0  0  0  0  0  0999 V2000
   -0.8444    2.5870    1.5141 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4107    1.5609    1.9475 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2086    1.1954    3.2686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2755    0.7675    1.0500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3880   -0.1844    0.2739 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1716   -1.0512   -0.6646 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4512   -1.5266   -0.1217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5866   -1.3245   -0.5950 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3995   -2.2856    1.0481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2865   -0.2820   -1.8592 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8892    0.1541   -2.0259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4941    0.5961   -0.6017 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9304    0.3570   -0.4802 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4801   -0.9006   -0.4541 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8511   -1.0713   -0.3366 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6932    0.0358   -0.2429 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1244   -0.0812   -0.1184 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6627   -1.2060   -0.0913 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9057    1.0472   -0.0286 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1326    1.2482   -0.2707 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7840    1.4340   -0.3860 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0379    0.7974    3.7378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9854    0.2118    1.7113 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8860    1.3992    0.3727 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8823   -0.8082    1.0367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5570   -1.9483   -0.8904 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0788   -3.2425    1.0811 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8810    0.5681   -1.7600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3286   -0.7572   -2.3181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7820    0.9559   -2.7513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7250    1.7006   -0.6043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8471   -1.7438   -0.5247 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3089   -2.0547   -0.3136 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3667    1.3853    0.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    2.4665   -0.3957 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 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  2  0
 16 20  1  0
 20 21  2  0
 16 17  1  0
 17 19  1  0
 17 18  2  0
  6  7  1  0
  7  9  1  0
  7  8  2  0
 12  5  1  0
 21 13  1  0
  3 22  1  0
  4 23  1  0
  4 24  1  0
  5 25  1  1
  6 26  1  6
 10 28  1  0
 11 29  1  0
 11 30  1  0
 12 31  1  6
 14 32  1  0
 15 33  1  0
 21 35  1  0
 19 34  1  0
  9 27  1  0
M  END


  Mrv1533004191521492D          

 21 22  0  0  0  0            999 V2000
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3507   -2.0195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1353   -1.7646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3068   -0.9576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6937   -0.4056    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9091   -0.6605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0915   -0.7027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7045   -1.2547    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2630    0.1043    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1665   -1.4675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7796   -2.0195    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3381   -0.6605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  5  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
 13 16  1  0  0  0  0
 16 17  2  0  0  0  0
 16 18  1  0  0  0  0
  6 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0253843

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC1C(NCC1C1=CC=C(N=C1)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H14N2O6/c16-10(17)3-7-8(5-15-11(7)13(20)21)6-1-2-9(12(18)19)14-4-6/h1-2,4,7-8,11,15H,3,5H2,(H,16,17)(H,18,19)(H,20,21)

> <INCHI_KEY>
GOUSHYKCXZKVEY-UHFFFAOYSA-N

> <FORMULA>
C13H14N2O6

> <MOLECULAR_WEIGHT>
294.263

> <EXACT_MASS>
294.085186179

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.659072178515657

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid

> <ALOGPS_LOGP>
-1.24

> <JCHEM_LOGP>
-3.3082801018066856

> <ALOGPS_LOGS>
-2.18

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
0.9865118449883976

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.23578363563198756

> <JCHEM_PKA_STRONGEST_BASIC>
11.442613962762145

> <JCHEM_POLAR_SURFACE_AREA>
136.82

> <JCHEM_REFRACTIVITY>
68.0962

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.93e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.580  -3.215   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.104  -4.680   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.377  -2.739   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.521  -3.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.986  -3.294   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.306  -1.788   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -3.162  -0.757   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -1.697  -1.233   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.771  -1.312   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -6.915  -2.342   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -6.091   0.195   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.044  -2.739   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.189  -3.770   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       4.364  -1.233   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    9                                                  
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    5   10                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14   10                                                       
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19    6   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END

View in JSmol

Synonyms

Value	Source
5-[5-Carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylate	Generator

Chemical Formula

C₁₃H₁₄N₂O₆

Average Mass

294.2630 Da

Monoisotopic Mass

294.08519 Da

IUPAC Name

5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid

Traditional Name

5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1C(NCC1C1=CC=C(N=C1)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C13H14N2O6/c16-10(17)3-7-8(5-15-11(7)13(20)21)6-1-2-9(12(18)19)14-4-6/h1-2,4,7-8,11,15H,3,5H2,(H,16,17)(H,18,19)(H,20,21)

InChI Key

GOUSHYKCXZKVEY-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
Clitocybe acromelalga	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as kainoids. These are non-proteigenous amino acids with a structure characterized by the presence of a pyrrolidine ring bearing two dicarboxylic acid groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Kainoids

Alternative Parents

Substituents

Kainoid skeleton
Proline or derivatives
Pyrrolidinylpyridine
Alpha-amino acid
5-alkyl-2-carboxypyrimidine
Alpha-amino acid or derivatives
Pyridine carboxylic acid
Pyridine carboxylic acid or derivatives
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
Aralkylamine
Dicarboxylic acid or derivatives
Pyridine
Pyrrolidine
Heteroaromatic compound
Amino acid
Azacycle
Secondary amine
Organoheterocyclic compound
Carboxylic acid
Secondary aliphatic amine
Organic oxygen compound
Organic oxide
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Carbonyl group
Amine
Hydrocarbon derivative
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	-1.2	ALOGPS
logP	-3.3	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	0.24	ChemAxon
pKa (Strongest Basic)	11.44	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	136.82 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	68.1 m³·mol⁻¹	ChemAxon
Polarizability	27.66 Å³	ChemAxon
Number of Rings	2	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

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

71317514

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid (NP0253843)

MOL for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

3D MOL for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

3D SDF for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

3D-SDF for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

PDB for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

3D PDB for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

SMILES for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

INCHI for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

Structure for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)

3D Structure for NP0253843 (5-[5-carboxy-4-(carboxymethyl)pyrrolidin-3-yl]pyridine-2-carboxylic acid)