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Showing metabocard for 1-Piperideine-2-carboxylic acid (HMDB0001084)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:25 UTC
HMDB IDHMDB0001084
Secondary Accession Numbers
  • HMDB0062778
  • HMDB01084
  • HMDB62778
Metabolite Identification
Common Name1-Piperideine-2-carboxylic acid
Description1-Piperideine-2-carboxylic acid (P2C), also known as Δ1-pipecolic acid, is classified as a member of the tetrahydropyridines. Tetrahydropyridines are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. 1-Piperideine-2-carboxylic acid is considered to be slightly soluble (in water) and acidic. 1-Piperideine-2-carboxylic acid is an intermediate of the L-lysine metabolic pathway in the brain; the uptake of P2C into the synaptosome of the cerebral cortex was Na+ and temperature-dependent (PMID: 7654748 ).
Structure
Data?1676999725
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001084 (1-Piperideine-2-carboxylic acid)


  Mrv1652305171818282D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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
    1.4289    0.8250    0.0000 N   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 C   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
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  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  3  1  0  0  0  0
  9  1  1  0  0  0  0
M  END
Download

3D MOL for HMDB0001084 (1-Piperideine-2-carboxylic acid)

HMDB0001084
     RDKit          3D
1-Piperideine-2-carboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3148   -1.5233    1.6658 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967   -0.7481    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1976   -0.2080    0.0603 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7455   -0.4427    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.9419    0.8608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6384   -0.7228    0.5437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    0.2818   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6974    1.2926   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5564    0.4739   -0.8720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0929   -0.6779    0.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2066   -0.3740    1.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -1.6672    0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8276    0.7657   -0.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7097   -0.2545   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8414    2.1242   -1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6209    1.6086    0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3324   -0.1409   -1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4132    1.1545   -1.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
Download

3D SDF for HMDB0001084 (1-Piperideine-2-carboxylic acid)


  Mrv1652305171818282D          

  9  9  0  0  0  0            999 V2000
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   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
    1.4289    0.8250    0.0000 N   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 C   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
    1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  3  4  2  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  3  1  0  0  0  0
  9  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001084

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=NCCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)

> <INCHI_KEY>
GEJXSVNGWOSZPC-UHFFFAOYSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.1412

> <EXACT_MASS>
127.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.836279738869656

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4,5,6-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
0.65

> <JCHEM_LOGP>
0.9737831613333332

> <ALOGPS_LOGS>
-1.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.088259725140425

> <JCHEM_PKA_STRONGEST_BASIC>
1.8931989193157819

> <JCHEM_POLAR_SURFACE_AREA>
49.660000000000004

> <JCHEM_REFRACTIVITY>
32.4398

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-piperideine-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001084 (1-Piperideine-2-carboxylic acid)

HMDB0001084
     RDKit          3D
1-Piperideine-2-carboxylic acid
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.3148   -1.5233    1.6658 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0967   -0.7481    0.6957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1976   -0.2080    0.0603 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7455   -0.4427    0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2478   -0.9419    0.8608 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6384   -0.7228    0.5437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8305    0.2818   -0.5695 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6974    1.2926   -0.5290 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5564    0.4739   -0.8720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0929   -0.6779    0.0740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2066   -0.3740    1.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1294   -1.6672    0.2100 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8276    0.7657   -0.5030 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7097   -0.2545   -1.5479 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8414    2.1242   -1.2111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6209    1.6086    0.5447 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3324   -0.1409   -1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4132    1.1545   -1.0350 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  6 11  1  0
  6 12  1  0
  7 13  1  0
  7 14  1  0
  8 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0001084 (1-Piperideine-2-carboxylic acid)

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       2.667   1.540   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    3    9                                                  
CONECT    2    1                                                            
CONECT    3    1    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3                                                       
CONECT    9    1                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0001084 (1-Piperideine-2-carboxylic acid)

COMPND    HMDB0001084
HETATM    1  O1  UNL     1       2.315  -1.523   1.666  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.097  -0.748   0.696  1.00  0.00           C  
HETATM    3  O2  UNL     1       3.198  -0.208   0.060  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.746  -0.443   0.273  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.248  -0.942   0.861  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.638  -0.723   0.544  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.831   0.282  -0.569  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.697   1.293  -0.529  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.556   0.474  -0.872  1.00  0.00           C  
HETATM   10  H1  UNL     1       4.093  -0.678   0.074  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.207  -0.374   1.432  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.129  -1.667   0.210  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.828   0.766  -0.503  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.710  -0.254  -1.548  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.841   2.124  -1.211  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.621   1.609   0.545  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.332  -0.141  -1.788  1.00  0.00           H  
HETATM   18  H9  UNL     1       1.413   1.155  -1.035  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    5    9
CONECT    5    6
CONECT    6    7   11   12
CONECT    7    8   13   14
CONECT    8    9   15   16
CONECT    9   17   18
END
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SMILES for HMDB0001084 (1-Piperideine-2-carboxylic acid)

OC(=O)C1=NCCCC1
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INCHI for HMDB0001084 (1-Piperideine-2-carboxylic acid)

InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,2-Didehydropiperidine-2-carboxylateChEBI
Delta(1)-Piperidine-2-carboxylic acidChEBI
1-Piperideine-2-carboxylateKegg
1,2-Didehydropiperidine-2-carboxylic acidGenerator
delta(1)-Piperidine-2-carboxylateGenerator
Δ(1)-piperidine-2-carboxylateGenerator
Δ(1)-piperidine-2-carboxylic acidGenerator
D-1-Piperideine-2-carboxylateHMDB
delta(1)-Piperideine-2-carboxylateHMDB
Delta1-Piperideine-2-carboxylateHMDB
1-p-2-CAHMDB
delta 1-Piperideine-2-carboxylateHMDB
delta1-Piperideine-2-carboxylic acidHMDB
Δ1-piperideine-2-carboxylateHMDB
Δ1-piperideine-2-carboxylic acidHMDB
3,4,5,6-Tetrahydro-2-pyridinecarboxylateHMDB
3,4,5,6-Tetrahydro-2-pyridinecarboxylic acidHMDB
D-1-Piperideine-2-carboxylic acidHMDB
delta1-Pipecolic acidHMDB
delta1-Piperidine-2-carboxylateHMDB
delta1-Piperidine-2-carboxylic acidHMDB
Δ1-pipecolic acidHMDB
Δ1-piperidine-2-carboxylateHMDB
Δ1-piperidine-2-carboxylic acidHMDB
P2CHMDB
1-Piperideine-2-carboxylic acidGenerator
Chemical FormulaC6H9NO2
Average Molecular Weight127.1412
Monoisotopic Molecular Weight127.063328537
IUPAC Name3,4,5,6-tetrahydropyridine-2-carboxylic acid
Traditional Name1-piperideine-2-carboxylate
CAS Registry Number2756-89-0
SMILES
OC(=O)C1=NCCCC1
InChI Identifier
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H2,(H,8,9)
InChI KeyGEJXSVNGWOSZPC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassHydropyridines
Direct ParentTetrahydropyridines
Alternative Parents
Substituents
  • Tetrahydropyridine
  • Ketimine
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Imine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility5.18 g/LALOGPS
logP0.65ALOGPS
logP0.97ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)4.09ChemAxon
pKa (Strongest Basic)1.89ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area49.66 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability12.84 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+126.54931661259
DarkChem[M+H]+126.54931661259
DarkChem[M-H]-120.93831661259
DarkChem[M-H]-120.93831661259
AllCCS[M+H]+126.34532859911
AllCCS[M-H]-124.71532859911
DeepCCS[M+H]+133.76530932474
DeepCCS[M-H]-131.24830932474
DeepCCS[M-2H]-167.05330932474
DeepCCS[M+Na]+142.24430932474
AllCCS[M+H]+126.332859911
AllCCS[M+H-H2O]+121.632859911
AllCCS[M+NH4]+130.832859911
AllCCS[M+Na]+132.132859911
AllCCS[M-H]-124.732859911
AllCCS[M+Na-2H]-126.832859911
AllCCS[M+HCOO]-129.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.72 minutes32390414
Predicted by Siyang on May 30, 20229.8026 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.5 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid147.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-Piperideine-2-carboxylic acidOC(=O)C1=NCCCC12000.0Standard polar33892256
1-Piperideine-2-carboxylic acidOC(=O)C1=NCCCC11199.6Standard non polar33892256
1-Piperideine-2-carboxylic acidOC(=O)C1=NCCCC11232.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-Piperideine-2-carboxylic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)C1=NCCCC11321.9Semi standard non polar33892256
1-Piperideine-2-carboxylic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=NCCCC11526.2Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Peroxisome
Biospecimen LocationsNot Available
Tissue Locations
  • Brain
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022415
KNApSAcK IDNot Available
Chemspider ID1157
KEGG Compound IDC04092
BioCyc IDNot Available
BiGG ID35015
Wikipedia LinkNot Available
METLIN ID5992
PubChem Compound1194
PDB IDNot Available
ChEBI ID30912
Food Biomarker OntologyNot Available
VMH ID1PIPDN2C
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNoguchi, Yuichi; Kanda, Kiyoo; Hosoda, Taku; Akiyama, Katsumi. D1-Piperidine-2-carboxylic acid isolation from fermentatin broth. Jpn. Tokkyo Koho (1971), 5 pp.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Chang YF, Charles AK: Uptake and metabolism of delta 1-piperidine-2-carboxylic acid by synaptosomes from rat cerebral cortex. Biochim Biophys Acta. 1995 Aug 23;1238(1):29-33. [PubMed:7654748 ]

Enzymes

Enzyme Details
1. Peroxisomal sarcosine oxidase
General function:
Involved in oxidoreductase activity
Specific function:
Metabolizes sarcosine, L-pipecolic acid and L-proline.
Gene Name:
PIPOX
Uniprot ID:
Q9P0Z9
Molecular weight:
44065.515