Hmdb loader

Showing metabocard for N-Methylpiperidine (HMDB0243944)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:09:15 UTC
Update Date2021-09-26 22:51:20 UTC
HMDB IDHMDB0243944
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-Methylpiperidine
Description1-methylpiperidine belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms. 1-methylpiperidine is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). N-methylpiperidine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-Methylpiperidine 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0243944 (N-Methylpiperidine)


  Mrv1533004241515252D          

  7  7  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
    0.7145    1.2375    0.0000 N   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 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  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  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
Download

3D MOL for HMDB0243944 (N-Methylpiperidine)

HMDB0243944
     RDKit          3D
N-Methylpiperidine
 20 20  0  0  0  0  0  0  0  0999 V2000
    1.9823   -0.4706   -0.4300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0464   -0.0929    0.5831 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0401   -1.0950    0.8513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8593   -1.1247   -0.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6144    0.1667   -0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9140    1.3390    0.1365 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5154    1.2152    0.4460 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0133   -0.5878   -0.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0330    0.3403   -1.2089 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7538   -1.3951   -0.9603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5551   -0.7398    1.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -2.0574    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5300   -1.9970   -0.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2501   -1.1965   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9114    0.3148   -1.4883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6019   -0.0210    0.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4729    1.6879    1.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0495    2.1957   -0.5890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1454    1.7553   -0.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7528    1.7629    1.4064 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
M  END
Download

3D SDF for HMDB0243944 (N-Methylpiperidine)


  Mrv1533004241515252D          

  7  7  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
    0.7145    1.2375    0.0000 N   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 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  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  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0243944

> <DATABASE_NAME>
hmdb

> <SMILES>
CN1CCCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H13N/c1-7-5-3-2-4-6-7/h2-6H2,1H3

> <INCHI_KEY>
PAMIQIKDUOTOBW-UHFFFAOYSA-N

> <FORMULA>
C6H13N

> <MOLECULAR_WEIGHT>
99.177

> <EXACT_MASS>
99.104799423

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
12.529900476934078

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-methylpiperidine

> <ALOGPS_LOGP>
1.31

> <JCHEM_LOGP>
1.0405355973333332

> <ALOGPS_LOGS>
0.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.80831175795189

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
32.1301

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.25e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-methylpiperidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0243944 (N-Methylpiperidine)

HMDB0243944
     RDKit          3D
N-Methylpiperidine
 20 20  0  0  0  0  0  0  0  0999 V2000
    1.9823   -0.4706   -0.4300 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0464   -0.0929    0.5831 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0401   -1.0950    0.8513 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8593   -1.1247   -0.3560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6144    0.1667   -0.4080 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9140    1.3390    0.1365 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5154    1.2152    0.4460 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0133   -0.5878   -0.0069 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0330    0.3403   -1.2089 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7538   -1.3951   -0.9603 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5551   -0.7398    1.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4763   -2.0574    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5300   -1.9970   -0.3541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2501   -1.1965   -1.2870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9114    0.3148   -1.4883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6019   -0.0210    0.1086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4729    1.6879    1.0548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0495    2.1957   -0.5890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1454    1.7553   -0.3214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7528    1.7629    1.4064 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
  7 19  1  0
  7 20  1  0
M  END
Download

PDB for HMDB0243944 (N-Methylpiperidine)

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   3.850   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       1.334   2.310   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
Download

3D PDB for HMDB0243944 (N-Methylpiperidine)

COMPND    HMDB0243944
HETATM    1  C1  UNL     1       1.982  -0.471  -0.430  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.046  -0.093   0.583  1.00  0.00           N  
HETATM    3  C2  UNL     1       0.040  -1.095   0.851  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.859  -1.125  -0.356  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.614   0.167  -0.408  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.914   1.339   0.136  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.515   1.215   0.446  1.00  0.00           C  
HETATM    8  H1  UNL     1       3.013  -0.588  -0.007  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.033   0.340  -1.209  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.754  -1.395  -0.960  1.00  0.00           H  
HETATM   11  H4  UNL     1      -0.555  -0.740   1.719  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.476  -2.057   1.104  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.530  -1.997  -0.354  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.250  -1.196  -1.287  1.00  0.00           H  
HETATM   15  H8  UNL     1      -1.911   0.315  -1.488  1.00  0.00           H  
HETATM   16  H9  UNL     1      -2.602  -0.021   0.109  1.00  0.00           H  
HETATM   17  H10 UNL     1      -1.473   1.688   1.055  1.00  0.00           H  
HETATM   18  H11 UNL     1      -1.049   2.196  -0.589  1.00  0.00           H  
HETATM   19  H12 UNL     1       1.145   1.755  -0.321  1.00  0.00           H  
HETATM   20  H13 UNL     1       0.753   1.763   1.406  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    7
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6    7   17   18
CONECT    7   19   20
END
Download

SMILES for HMDB0243944 (N-Methylpiperidine)

CN1CCCCC1
Download

INCHI for HMDB0243944 (N-Methylpiperidine)

InChI=1S/C6H13N/c1-7-5-3-2-4-6-7/h2-6H2,1H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
1-Methyl-piperidineChEMBL
N-MethylpiperidineMeSH
N-Methylpiperidine hydrochlorideMeSH
Chemical FormulaC6H13N
Average Molecular Weight99.177
Monoisotopic Molecular Weight99.104799423
IUPAC Name1-methylpiperidine
Traditional NameN-methylpiperidine
CAS Registry NumberNot Available
SMILES
CN1CCCCC1
InChI Identifier
InChI=1S/C6H13N/c1-7-5-3-2-4-6-7/h2-6H2,1H3
InChI KeyPAMIQIKDUOTOBW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPiperidines
Sub ClassNot Available
Direct ParentPiperidines
Alternative Parents
Substituents
  • Piperidine
  • Tertiary aliphatic amine
  • Tertiary amine
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
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
logP1.31ALOGPS
logP1.04ChemAxon
logS0.1ALOGPS
pKa (Strongest Basic)9.81ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area3.24 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity32.13 m³·mol⁻¹ChemAxon
Polarizability12.53 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]+127.08230932474
DeepCCS[M-H]-125.00130932474
DeepCCS[M-2H]-160.43930932474
DeepCCS[M+Na]+135.11330932474
AllCCS[M+H]+117.932859911
AllCCS[M+H-H2O]+112.832859911
AllCCS[M+NH4]+122.632859911
AllCCS[M+Na]+124.032859911
AllCCS[M-H]-125.332859911
AllCCS[M+Na-2H]-128.532859911
AllCCS[M+HCOO]-132.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-MethylpiperidineCN1CCCCC1930.3Standard polar33892256
N-MethylpiperidineCN1CCCCC1740.8Standard non polar33892256
N-MethylpiperidineCN1CCCCC1765.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylpiperidine GC-MS (Non-derivatized) - 70eV, Positivesplash10-006t-9000000000-b00c4518168654acc9602021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - N-Methylpiperidine 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 - N-Methylpiperidine 10V, Positive-QTOFsplash10-0udi-0900000000-ce32e2fba4e783e784302016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 20V, Positive-QTOFsplash10-0udi-3900000000-608a25ed30874f020bd12016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 40V, Positive-QTOFsplash10-001i-9000000000-d745e1f7b8f59de31ba42016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 10V, Negative-QTOFsplash10-0002-9000000000-0fd0f93c22e59fff966c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 20V, Negative-QTOFsplash10-0002-9000000000-3d975be4d7d072c2bafc2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 40V, Negative-QTOFsplash10-067i-9000000000-3eadbeb008c7da7a2d4a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 10V, Positive-QTOFsplash10-0udi-0900000000-2cb596f269ee031d22f42021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 20V, Positive-QTOFsplash10-0udi-3900000000-82f2408d3f8d60c047202021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 40V, Positive-QTOFsplash10-0002-9000000000-ca7e115e1d7a56085a462021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 10V, Negative-QTOFsplash10-0002-9000000000-9026c27716a0406167922021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 20V, Negative-QTOFsplash10-0002-9000000000-9026c27716a0406167922021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - N-Methylpiperidine 40V, Negative-QTOFsplash10-0002-9000000000-8897d2c2d1dee8e1c3382021-10-12Wishart 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 IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12291
PDB IDNot Available
ChEBI IDNot Available
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 ]