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Showing NP-Card for (2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid (NP0296269)

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Record Information
Version2.0
Created at2022-09-10 05:44:46 UTC
Updated at2022-09-10 05:44:47 UTC
NP-MRD IDNP0296269
Secondary Accession NumbersNone
Natural Product Identification
Common Name(2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid
Description​2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid, also known as delta1-piperideine-6-L-carboxylate or (S)-2,3,4,5-tetrahydropyridine-2-carboxylate, belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. The (S)-enantiomer of 1-piperideine-6-carboxylic acid. ​2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid is a very strong basic compound (based on its pKa). (2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid is found in Streptomyces clavuligerus. ​2,3,4,5-Tetrahydro-2-pyridinecarboxylic acid exists in all living organisms, ranging from bacteria to humans.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)


  Mrv1652307191923512D          

  9  9  0  0  0  0            999 V2000
   -2.0758    0.2669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.1455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.9706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0758   -1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.9706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3613   -0.1455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -2.2081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0675   -0.9707    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  7  1  6  0  0  0
  7  9  1  0  0  0  0
  7  8  2  0  0  0  0
  1  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
Download

3D MOL for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)

     RDKit          3D

 18 18  0  0  0  0  0  0  0  0999 V2000
    2.8415    0.2912    1.2909 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2204   -0.1220    0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8603   -0.9864   -0.6054 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8306    0.2936   -0.0310 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0833    0.0500    1.1466 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5190   -0.1084    0.7933 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8347    0.1705   -0.6556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8136   -0.3994   -1.5620 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3984   -0.3159   -1.2269 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7653   -0.7450   -1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8640    1.4051   -0.1670 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2631   -0.8817    1.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427    0.8587    1.9207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8903   -1.1236    1.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1264    0.5949    1.3940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8227   -0.2696   -0.8980 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8967    1.2545   -0.8540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0995   -0.8741   -2.4859 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  2  0
  9  4  1  0
  3 10  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)


  Mrv1652307191923512D          

  9  9  0  0  0  0            999 V2000
   -2.0758    0.2669    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.1455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7903   -0.9706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0758   -1.3830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.9706    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3613   -0.1455    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -1.3831    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6469   -2.2081    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0675   -0.9707    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  7  1  6  0  0  0
  7  9  1  0  0  0  0
  7  8  2  0  0  0  0
  1  6  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0296269

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@@H]1CCCC=N1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1

> <INCHI_KEY>
CSDPVAKVEWETFG-YFKPBYRVSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.1412

> <EXACT_MASS>
127.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.691354980800693

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
-1.8274562075723537

> <ALOGPS_LOGS>
-1.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.0027714730041635

> <JCHEM_PKA_STRONGEST_BASIC>
6.217105927847416

> <JCHEM_POLAR_SURFACE_AREA>
49.66

> <JCHEM_REFRACTIVITY>
31.9983

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.53e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)

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PDB for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)
HEADER    PROTEIN                                 19-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUL-19         0                                  
HETATM    1  C   UNK     0      -3.875   0.498   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.209  -0.272   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.209  -1.812   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.875  -2.582   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.541  -1.812   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.541  -0.272   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -1.208  -2.582   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.208  -4.122   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.126  -1.812   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    7    6                                                  
CONECT    6    1    5                                                       
CONECT    7    5    9    8                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)
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SMILES for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)
OC(=O)[C@@H]1CCCC=N1
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INCHI for NP0296269 ((2s)-2,3,4,5-tetrahydropyridine-2-carboxylic acid)
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1
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View in JSmol
Synonyms
ValueSource
(S)-2,3,4,5-Tetrahydropyridine-2-carboxylic acidChEBI
delta1-Piperideine-6-L-carboxylateChEBI
Delta(1)-Piperideine-6-L-carboxylic acidChEBI
(S)-2,3,4,5-Tetrahydropyridine-2-carboxylateGenerator
delta1-Piperideine-6-L-carboxylic acidGenerator
Δ1-piperideine-6-L-carboxylateGenerator
Δ1-piperideine-6-L-carboxylic acidGenerator
delta(1)-Piperideine-6-L-carboxylateGenerator
Δ(1)-piperideine-6-L-carboxylateGenerator
Δ(1)-piperideine-6-L-carboxylic acidGenerator
​2,3,4,5-tetrahydro-2-pyridinecarboxylateGenerator
(S)-1-Piperideine-6-carboxylateHMDB
(2S)-2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
(S)-2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
(S)-2,3,4,5-Tetrahydropiperidine-2-carboxylateHMDB
(S)-2,3,4,5-Tetrahydropiperidine-2-carboxylic acidHMDB
1-Piperideine-6-carboxylateHMDB
1-Piperideine-6-carboxylic acidHMDB
2,3,4,5-Tetrahydro-2-pyridinecarboxylic acidHMDB
2,3,4,5-Tetrahydropicolinic acidHMDB
delta1-Piperideine-6-carboxylateHMDB
delta1-Piperideine-6-carboxylic acidHMDB
delta1-Piperidine-6-carboxylateHMDB
delta1-Piperidine-6-carboxylic acidHMDB
Δ1-piperidine-6-carboxylateHMDB
Δ1-piperidine-6-carboxylic acidHMDB
Δ1-piperideine-6-carboxylateHMDB
Δ1-piperideine-6-carboxylic acidHMDB
Chemical FormulaC6H9NO2
Average Mass127.1412 Da
Monoisotopic Mass127.06333 Da
IUPAC Name(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid
Traditional Name(2S)-2,3,4,5-tetrahydropyridine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)[C@@H]1CCCC=N1
InChI Identifier
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h4-5H,1-3H2,(H,8,9)/t5-/m0/s1
InChI KeyCSDPVAKVEWETFG-YFKPBYRVSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces clavuligerusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids and derivatives  
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
    • 

  • Tetrahydropyridine
    • 

  • Hydropyridine
    • 

  • Azacycle
    • 

  • Organoheterocyclic compound
    • 

  • Organic 1,3-dipolar compound
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Imine
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.36ALOGPS
logP-1.8ChemAxon
logS-1.2ALOGPS
pKa (Strongest Acidic)2ChemAxon
pKa (Strongest Basic)6.22ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.66 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32 m³·mol⁻¹ChemAxon
Polarizability12.69 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012130  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID21865623  
KEGG Compound IDC00450  
BioCyc IDCPD-7682  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound24771808  
PDB IDNot Available
ChEBI ID49014  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]