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Showing metabocard for 1-Piperideine (HMDB0243998)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:12:09 UTC
Update Date2021-09-26 22:51:26 UTC
HMDB IDHMDB0243998
Secondary Accession NumbersNone
Metabolite Identification
Common Name1-Piperideine
Description1-Piperideine 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. 1-Piperideine is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on 1-Piperideine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-piperideine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Piperideine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0243998 (1-Piperideine)


  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 HMDB0243998 (1-Piperideine)

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 HMDB0243998 (1-Piperideine)


  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>
HMDB0243998

> <DATABASE_NAME>
hmdb

> <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 HMDB0243998 (1-Piperideine)

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 HMDB0243998 (1-Piperideine)

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 HMDB0243998 (1-Piperideine)

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 HMDB0243998 (1-Piperideine)

C1CCN=CC1
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INCHI for HMDB0243998 (1-Piperideine)

InChI=1S/C5H9N/c1-2-4-6-5-3-1/h4H,1-3,5H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Delta(1)-PiperideineChEBI
PiperideineChEBI
Δ(1)-piperideineGenerator
Chemical FormulaC5H9N
Average Molecular Weight83.134
Monoisotopic Molecular Weight83.073499294
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
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
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Imine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP1.63ALOGPS
logP0.53ChemAxon
logS-1.5ALOGPS
pKa (Strongest Basic)10.21ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.17 m³·mol⁻¹ChemAxon
Polarizability9.7 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+122.1330932474
DeepCCS[M-H]-120.23430932474
DeepCCS[M-2H]-155.78330932474
DeepCCS[M+Na]+130.23730932474
AllCCS[M+H]+115.732859911
AllCCS[M+H-H2O]+110.432859911
AllCCS[M+NH4]+120.632859911
AllCCS[M+Na]+122.132859911
AllCCS[M-H]-120.532859911
AllCCS[M+Na-2H]-124.232859911
AllCCS[M+HCOO]-128.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-PiperideineC1CCN=CC11210.4Standard polar33892256
1-PiperideineC1CCN=CC1751.0Standard non polar33892256
1-PiperideineC1CCN=CC1742.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1-Piperideine GC-MS (Non-derivatized) - 70eV, Positivesplash10-001l-9000000000-4f31805ce26192d9d6232021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1-Piperideine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 10V, Positive-QTOFsplash10-001i-9000000000-72c8691eb15dce6e0abb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 20V, Positive-QTOFsplash10-001l-9000000000-1356d182311c252982de2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 40V, Positive-QTOFsplash10-052f-9000000000-a58a0919c5cd868e826b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 10V, Negative-QTOFsplash10-001i-9000000000-34725d39e59b81eb78242021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 20V, Negative-QTOFsplash10-001i-9000000000-34725d39e59b81eb78242021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1-Piperideine 40V, Negative-QTOFsplash10-001i-9000000000-788abf5a93ba6dffb4b72021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00051878
Chemspider ID61469
KEGG Compound IDC06181
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID47858
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]