Hmdb loader

Showing metabocard for Piperidine (HMDB0034301)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 19:06:26 UTC
Update Date2023-02-21 17:24:09 UTC
HMDB IDHMDB0034301
Secondary Accession Numbers
  • HMDB34301
Metabolite Identification
Common NamePiperidine
DescriptionPiperidine is an organic compound with the molecular formula (CH2)5NH. This heterocyclic amine consists of a six-membered ring containing five methylene units and one nitrogen atom. Piperdine is a member of the class of compounds known as azacycloalkane. An azacyloalkane is cyclohexane in which one of the carbons is replaced by a nitrogen. Piperdine is a naturally occurring metabolite in the human body. In particular, it is a metabolite of cadaverine, a polyamine found in the human intestine and other mammalian intestines (PMID: 6406679 ). Piperidine is considered to be a microbial metabolite. Piperdine can be isolated from a variety of natural sources or synthesized in the lab and exists as a colorless fuming liquid with an odor described as ammoniacal or pepper-like. The name piperdine comes from the genus name Piper, which is the Latin word for pepper. Piperidine is found in a number of plants including black pepper (Piper nigrum), celery plants, bell peppers and tobacco. The piperidine structural motif is present in numerous natural alkaloids. These include piperine, which gives black pepper its spicy taste. In food, piperidine is a flavouring agent and it is also widely used as a building block and chemical reagent in the synthesis of organic compounds, including pharmaceuticals. As a liquid, piperidine is used as a solvent and as a base. 
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034301 (Piperidine)

  Mrv1652303202019012D          

  6  6  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   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    0.0000    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0034301 (Piperidine)

HMDB0034301
     RDKit          3D
Piperidine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.3400   -0.2936   -0.0350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2031   -1.1865   -0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9447   -0.9727    0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4257    0.3659    0.3761 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5282    1.2547   -0.3063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8460    1.0750    0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1770   -0.2570   -0.7480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7208   -0.8033    0.8967 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0832   -0.9692   -1.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5418   -2.2413   -0.4981 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7413   -1.6712    0.1635 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5260   -1.1709    1.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4165    0.4727    0.1296 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4107    1.0384   -1.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8836    2.2945   -0.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4778    1.8946   -0.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6533    1.1700    1.4459 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  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
M  END
Download

3D SDF for HMDB0034301 (Piperidine)

  Mrv1652303202019012D          

  6  6  0  0  0  0            999 V2000
    1.4289    0.8250    0.0000 C   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    0.0000    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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0034301

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CCNCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2

> <INCHI_KEY>
NQRYJNQNLNOLGT-UHFFFAOYSA-N

> <FORMULA>
C5H11N

> <MOLECULAR_WEIGHT>
85.1475

> <EXACT_MASS>
85.089149357

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
10.42557442244739

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperidine

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
0.6574876599999997

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
10.404363842628063

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
26.835399999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
piperidine

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0034301 (Piperidine)

HMDB0034301
     RDKit          3D
Piperidine
 17 17  0  0  0  0  0  0  0  0999 V2000
   -1.3400   -0.2936   -0.0350 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2031   -1.1865   -0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9447   -0.9727    0.4553 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4257    0.3659    0.3761 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5282    1.2547   -0.3063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8460    1.0750    0.3561 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1770   -0.2570   -0.7480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7208   -0.8033    0.8967 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0832   -0.9692   -1.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5418   -2.2413   -0.4981 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7413   -1.6712    0.1635 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5260   -1.1709    1.4663 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4165    0.4727    0.1296 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4107    1.0384   -1.3832 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8836    2.2945   -0.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4778    1.8946   -0.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6533    1.1700    1.4459 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  1  1  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  6 17  1  0
M  END
Download

PDB for HMDB0034301 (Piperidine)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   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  C   UNK     0       0.000   1.540   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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    4    5                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
Download

3D PDB for HMDB0034301 (Piperidine)

COMPND    HMDB0034301
HETATM    1  C1  UNL     1      -1.340  -0.294  -0.035  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.203  -1.186  -0.526  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.945  -0.973   0.455  1.00  0.00           C  
HETATM    4  N1  UNL     1       1.426   0.366   0.376  1.00  0.00           N  
HETATM    5  C4  UNL     1       0.528   1.255  -0.306  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.846   1.075   0.356  1.00  0.00           C  
HETATM    7  H1  UNL     1      -2.177  -0.257  -0.748  1.00  0.00           H  
HETATM    8  H2  UNL     1      -1.721  -0.803   0.897  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.083  -0.969  -1.563  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.542  -2.241  -0.498  1.00  0.00           H  
HETATM   11  H5  UNL     1       1.741  -1.671   0.163  1.00  0.00           H  
HETATM   12  H6  UNL     1       0.526  -1.171   1.466  1.00  0.00           H  
HETATM   13  H7  UNL     1       2.416   0.473   0.130  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.411   1.038  -1.383  1.00  0.00           H  
HETATM   15  H9  UNL     1       0.884   2.294  -0.226  1.00  0.00           H  
HETATM   16  H10 UNL     1      -1.478   1.895  -0.004  1.00  0.00           H  
HETATM   17  H11 UNL     1      -0.653   1.170   1.446  1.00  0.00           H  
CONECT    1    2    6    7    8
CONECT    2    3    9   10
CONECT    3    4   11   12
CONECT    4    5   13
CONECT    5    6   14   15
CONECT    6   16   17
END
Download

SMILES for HMDB0034301 (Piperidine)

C1CCNCC1
Download

INCHI for HMDB0034301 (Piperidine)

InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
AzacyclohexaneChEBI
AzinaneChEBI
CyclopentimineChEBI
CypentilChEBI
HexahydropyridineChEBI
HexazaneChEBI
PentamethyleneamineChEBI
PentamethyleneimineChEBI
PentamethylenimineChEBI
PerhydropyridineChEBI
pipChEBI
PiperidinChEBI
FEMA 2908HMDB
hexahydro-PyridineHMDB
Piperidine ON rasta resinHMDB
Chemical FormulaC5H11N
Average Molecular Weight85.1475
Monoisotopic Molecular Weight85.089149357
IUPAC Namepiperidine
Traditional Namepiperidine
CAS Registry Number110-89-4
SMILES
C1CCNCC1
InChI Identifier
InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2
InChI KeyNQRYJNQNLNOLGT-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 Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-9 °CNot Available
Boiling Point106.00 to 107.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000 mg/mL at 20 °CNot Available
LogP0.84Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
Metastatic melanoma
  1. Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, Koh AY: Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients. Neoplasia. 2017 Oct;19(10):848-855. doi: 10.1016/j.neo.2017.08.004. Epub 2017 Sep 15. [PubMed:28923537 ]
Perillyl alcohol administration for cancer treatment
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Pancreatic cancer
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Periodontal disease
  1. Sugimoto M, Wong DT, Hirayama A, Soga T, Tomita M: Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics. 2010 Mar;6(1):78-95. Epub 2009 Sep 10. [PubMed:20300169 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012644
KNApSAcK IDC00051876
Chemspider ID7791
KEGG Compound IDC01746
BioCyc IDPIPERIDINE
BiGG IDNot Available
Wikipedia LinkPiperidine
METLIN IDNot Available
PubChem Compound8082
PDB IDPIP
ChEBI ID18049
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1009201
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. De Marco A, De Candia M, Carotti A, Cellamare S, De Candia E, Altomare C: Lipophilicity-related inhibition of blood platelet aggregation by nipecotic acid anilides. Eur J Pharm Sci. 2004 Jun;22(2-3):153-64. [PubMed:15158900 ]
  2. Dembitsky VM: Astonishing diversity of natural surfactants: 6. Biologically active marine and terrestrial alkaloid glycosides. Lipids. 2005 Nov;40(11):1081-105. [PubMed:16459921 ]
  3. Aisaka K, Hattori Y, Ishihara T, Morita M, Kase Y, Miyata T: The effects of piperidine and its related substances on blood vessels. Jpn J Pharmacol. 1985 Apr;37(4):345-53. [PubMed:4010086 ]
  4. Patel K, Chen Y, Dennehy K, Blau J, Connors S, Mendonca M, Tarpey M, Krishna M, Mitchell JB, Welch WJ, Wilcox CS: Acute antihypertensive action of nitroxides in the spontaneously hypertensive rat. Am J Physiol Regul Integr Comp Physiol. 2006 Jan;290(1):R37-43. Epub 2005 Sep 22. [PubMed:16179488 ]
  5. Nishi K, Iwasaki K, Kase Y: Actions of piperidine and dimethylphenylpiperazinium (DMPP) on afferent discharges of the cat's carotid body. Eur J Pharmacol. 1979 Feb 15;54(1-2):141-52. [PubMed:421736 ]
  6. Nomura Y, Schmidt-Glenewinkel T, Giacobini E, Ortiz J: Metabolism of cadaverine and pipecolic acid in brain and other organs of the mouse. J Neurosci Res. 1983;9(3):279-89. doi: 10.1002/jnr.490090305. [PubMed:6406679 ]
  7. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .