Showing metabocard for Piperideine (MMDBc0049864)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-04-29 22:45:04 UTC
Update Date2025-10-07 16:08:13 UTC
Metabolite IDMMDBc0049864
Metabolite Identification
Common NamePiperideine
DescriptionPiperideine is a cyclic amine belonging to the chemical class of piperidines. Its structure features a six-membered ring containing one nitrogen atom, which is crucial for its biological activity. Piperideine is involved in lysine catabolism, where it forms Δ1-piperideine-6-carboxylic acid (P6C), a metabolite that has been implicated in various neurological disorders, including pyridoxine-dependent epilepsy due to ALDH7A1 deficiency. This condition leads to the accumulation of toxic intermediates like α-aminoadipic semialdehyde and P6C, which can disrupt vitamin B6 homeostasis by sequestering its vitamers into inert complexes (PMID:40671330 ). Elevated levels of P6C are linked to neurological symptoms, making its quantification in biological fluids essential for diagnosis (PMID:39900492 ). Furthermore, piperideine-6-carboxylic acid has been shown to regulate vitamin B6 homeostasis and modulate systemic immunity in plants (PMID:40033073 ). The understanding of piperideine's role in these biochemical pathways underscores its significance in both human health and plant biology, highlighting the interconnectedness of metabolic processes across different organisms.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f2e50d16ef8>


  Mrv1533004241519242D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   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
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f2e50d16ef8>

HMDB0243998
     RDKit          3D
1-Piperideine
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.1990   -0.9129   -0.5366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0896   -1.5408   -0.7000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0385   -1.0681    0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1506    0.4302   -0.1989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787    1.1781    0.1906 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2255    0.2377    0.4052 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681   -1.2433   -1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9793   -1.5126   -0.3624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8816   -1.3182    1.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650    0.5142   -1.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0659    0.8287    0.2338 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3535    1.9490   -0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0887    1.7428    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1727    0.8003    0.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2824   -0.0852    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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3D SDF for #<Metabolite:0x00007f2e50d16ef8>


  Mrv1533004241519242D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   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
    0.7145   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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  2  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049864

> <DATABASE_NAME>
MIME

> <SMILES>
C1CCN=CC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9N/c1-2-4-6-5-3-1/h4H,1-3,5H2

> <INCHI_KEY>
DWKUKQRKVCMOLP-UHFFFAOYSA-N

> <FORMULA>
C5H9N

> <MOLECULAR_WEIGHT>
83.134

> <EXACT_MASS>
83.073499294

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.699907087792734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4,5-tetrahydropyridine

> <ALOGPS_LOGP>
1.63

> <JCHEM_LOGP>
0.5259472413333334

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.206131728545545

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
26.1684

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
piperideine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x00007f2e50d16ef8>

HMDB0243998
     RDKit          3D
1-Piperideine
 15 15  0  0  0  0  0  0  0  0999 V2000
    1.1990   -0.9129   -0.5366 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0896   -1.5408   -0.7000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0385   -1.0681    0.0518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1506    0.4302   -0.1989 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0787    1.1781    0.1906 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2255    0.2377    0.4052 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0681   -1.2433   -1.0879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9793   -1.5126   -0.3624 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8816   -1.3182    1.0993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2650    0.5142   -1.3194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0659    0.8287    0.2338 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3535    1.9490   -0.5599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0887    1.7428    1.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1727    0.8003    0.1737 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2824   -0.0852    1.4629 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  1  1  0
  1  7  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  6 15  1  0
M  END
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PDB for #<Metabolite:0x00007f2e50d16ef8>

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for #<Metabolite:0x00007f2e50d16ef8>

COMPND    HMDB0243998
HETATM    1  C1  UNL     1       1.199  -0.913  -0.537  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.090  -1.541  -0.700  1.00  0.00           N  
HETATM    3  C2  UNL     1      -1.038  -1.068   0.052  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.151   0.430  -0.199  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.079   1.178   0.191  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.226   0.238   0.405  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.068  -1.243  -1.088  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.979  -1.513  -0.362  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.882  -1.318   1.099  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.265   0.514  -1.319  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.066   0.829   0.234  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.353   1.949  -0.560  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.089   1.743   1.148  1.00  0.00           H  
HETATM   14  H8  UNL     1       2.173   0.800   0.174  1.00  0.00           H  
HETATM   15  H9  UNL     1       1.282  -0.085   1.463  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3
CONECT    3    4    8    9
CONECT    4    5   10   11
CONECT    5    6   12   13
CONECT    6   14   15
END
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SMILES for #<Metabolite:0x00007f2e50d16ef8>

C1CCN=CC1
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INCHI for #<Metabolite:0x00007f2e50d16ef8>

InChI=1S/C5H9N/c1-2-4-6-5-3-1/h4H,1-3,5H2
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Synonyms
ValueSource
Delta(1)-PiperideineChEBI
PiperideineChEBI
Δ(1)-piperideineGenerator
Molecular FormulaC5H9N
Average Mass83.134
Monoisotopic Mass83.073499294
IUPAC Name2,3,4,5-tetrahydropyridine
Traditional Namepiperideine
CAS Registry NumberNot Available
SMILES
C1CCN=CC1
InChI Identifier
InChI=1S/C5H9N/c1-2-4-6-5-3-1/h4H,1-3,5H2
InChI KeyDWKUKQRKVCMOLP-UHFFFAOYSA-N