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Showing metabocard for 2-Methylpiperidine (HMDB0032416)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:49:41 UTC
Update Date2023-02-21 17:22:07 UTC
HMDB IDHMDB0032416
Secondary Accession Numbers
  • HMDB32416
Metabolite Identification
Common Name2-Methylpiperidine
Description2-Methylpiperidine, also known as alpha -pipecolin or 2-pipecoline, 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. Based on a literature review a significant number of articles have been published on 2-Methylpiperidine.
Structure
Data?1677000127
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032416 (2-Methylpiperidine)

  Mrv1652304291919362D          

  7  7  0  0  0  0            999 V2000
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    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 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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  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
  1  7  1  0  0  0  0
M  END
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3D MOL for HMDB0032416 (2-Methylpiperidine)

HMDB0032416
     RDKit          3D
2-Methylpiperidine
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.1889    0.2624    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0398   -0.0853   -0.4552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2531   -1.2220    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2240   -1.1356   -0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8157    0.2079    0.0742 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8352    1.3394    0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3239    1.1112   -0.7242 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0905    1.3108    0.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1691    0.0556    0.0648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0872   -0.3818    1.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5367   -0.4001   -1.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5775   -2.1849   -0.4338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -1.3800    1.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6613   -1.8093    0.6932 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5844   -1.6079   -1.0658 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6040    0.3733   -0.7182 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3917    0.2961    1.0393 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5749    1.6406    1.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3688    2.2271   -0.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2555    1.3825   -1.7103 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
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
M  END
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3D SDF for HMDB0032416 (2-Methylpiperidine)

  Mrv1652304291919362D          

  7  7  0  0  0  0            999 V2000
    0.0000    0.8250    0.0000 N   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
    0.7145    2.0625    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 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
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  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
  1  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032416

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C6H13N/c1-6-4-2-3-5-7-6/h6-7H,2-5H2,1H3

> <INCHI_KEY>
NNWUEBIEOFQMSS-UHFFFAOYSA-N

> <FORMULA>
C6H13N

> <MOLECULAR_WEIGHT>
99.1741

> <EXACT_MASS>
99.104799421

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
12.500820009279266

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylpiperidine

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
1.0740626846666665

> <ALOGPS_LOGS>
-0.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.4816014438751

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
31.254199999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.43e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-methylpiperidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0032416 (2-Methylpiperidine)

HMDB0032416
     RDKit          3D
2-Methylpiperidine
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.1889    0.2624    0.4872 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0398   -0.0853   -0.4552 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2531   -1.2220    0.0621 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2240   -1.1356   -0.1042 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8157    0.2079    0.0742 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8352    1.3394    0.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3239    1.1112   -0.7242 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0905    1.3108    0.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1691    0.0556    0.0648 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0872   -0.3818    1.3979 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5367   -0.4001   -1.4207 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5775   -2.1849   -0.4338 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5380   -1.3800    1.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6613   -1.8093    0.6932 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5844   -1.6079   -1.0658 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6040    0.3733   -0.7182 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3917    0.2961    1.0393 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5749    1.6406    1.1046 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3688    2.2271   -0.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2555    1.3825   -1.7103 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
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
  5 17  1  0
  6 18  1  0
  6 19  1  0
  7 20  1  0
M  END
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PDB for HMDB0032416 (2-Methylpiperidine)

HEADER    PROTEIN                                 29-APR-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-19         0                                  
HETATM    1  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+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
CONECT    1    2    7                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    1                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0032416 (2-Methylpiperidine)

COMPND    HMDB0032416
HETATM    1  C1  UNL     1      -2.189   0.262   0.487  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.040  -0.085  -0.455  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.253  -1.222   0.062  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.224  -1.136  -0.104  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.816   0.208   0.074  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.835   1.339   0.058  1.00  0.00           C  
HETATM    7  N1  UNL     1      -0.324   1.111  -0.724  1.00  0.00           N  
HETATM    8  H1  UNL     1      -2.091   1.311   0.874  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.169   0.056   0.065  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.087  -0.382   1.398  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.537  -0.400  -1.421  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.577  -2.185  -0.434  1.00  0.00           H  
HETATM   13  H6  UNL     1      -0.538  -1.380   1.144  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.661  -1.809   0.693  1.00  0.00           H  
HETATM   15  H8  UNL     1       1.584  -1.608  -1.066  1.00  0.00           H  
HETATM   16  H9  UNL     1       2.604   0.373  -0.718  1.00  0.00           H  
HETATM   17  H10 UNL     1       2.392   0.296   1.039  1.00  0.00           H  
HETATM   18  H11 UNL     1       0.575   1.641   1.105  1.00  0.00           H  
HETATM   19  H12 UNL     1       1.369   2.227  -0.367  1.00  0.00           H  
HETATM   20  H13 UNL     1      -0.255   1.382  -1.710  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    7   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6   16   17
CONECT    6    7   18   19
CONECT    7   20
END
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SMILES for HMDB0032416 (2-Methylpiperidine)

CC1CCCCN1
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INCHI for HMDB0032416 (2-Methylpiperidine)

InChI=1S/C6H13N/c1-6-4-2-3-5-7-6/h6-7H,2-5H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Methyl-piperidineHMDB
(S)-(+)-2-MethylpiperidineHMDB
2-PipecolineHMDB
2-Pipecoline (8ci)HMDB
alpha -MethylpiperidineHMDB
alpha -PipecolinHMDB
alpha -PipecolineHMDB
alpha-MethylpiperidineHMDB
alpha-PipecolinHMDB
alpha-PipecolineHMDB
D-alpha-PipecolineHMDB
Pipecoline, alphaHMDB
PipicolineHMDB
2-Methylpiperidine hydrochlorideHMDB
2-Methylpiperidine, (+-)-isomerHMDB
Chemical FormulaC6H13N
Average Molecular Weight99.1741
Monoisotopic Molecular Weight99.104799421
IUPAC Name2-methylpiperidine
Traditional Name2-methylpiperidine
CAS Registry Number109-05-7
SMILES
CC1CCCCN1
InChI Identifier
InChI=1S/C6H13N/c1-6-4-2-3-5-7-6/h6-7H,2-5H2,1H3
InChI KeyNNWUEBIEOFQMSS-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
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point117.00 to 119.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility50930 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.148 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
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 IDFDB009857
KNApSAcK IDNot Available
Chemspider ID7686
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound7974
PDB IDNot Available
ChEBI ID535978
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1108251
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). EAFUS: Everything Added to Food in the United States.. .