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Showing metabocard for 2-Piperidinone (HMDB0011749)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-03-05 10:31:10 UTC
Update Date2023-02-21 17:17:36 UTC
HMDB IDHMDB0011749
Secondary Accession Numbers
  • HMDB11749
Metabolite Identification
Common Name2-Piperidinone
Description2-Piperidinone is a derivative of piperidine which is an organic compound. Piperidine is a colorless fuming liquid with an odor described as ammoniacal, pepper-like, the name comes from the genus name Piper, which is the Latin word for pepper. Piperidine is a widely used building block and chemical reagent in the synthesis of organic compounds, including pharmaceuticals.The piperidine structural motif is present in numerous natural alkaloids. These include piperine, which gives black pepper the hot taste. This gave the compound its name.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0011749 (2-Piperidinone)

  Mrv1652305261923552D          

  7  7  0  0  0  0            999 V2000
   10.8728   -8.8558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0479   -8.8558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2853   -9.5703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6355   -9.5703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8728  -10.2848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0479  -10.2848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.2853  -10.9994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
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3D MOL for HMDB0011749 (2-Piperidinone)

HMDB0011749
     RDKit          3D
2-Piperidinone
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3868    1.4900   -0.1212 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3294    0.8149   -0.0955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0158    1.4295   -0.2280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9563    0.6031    0.6451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0679   -0.7574    0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2480   -1.3887   -0.3021 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3874   -0.6023    0.0662 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0533    2.4729    0.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3227    1.3469   -1.2763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5817    0.5618    1.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9378    1.1089    0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7363   -1.4074    0.6351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6039   -0.5895   -0.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.6214   -1.3969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3191   -2.3881    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2480   -1.0731    0.4489 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  7  1  0
  7  2  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
  7 16  1  0
M  END
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3D SDF for HMDB0011749 (2-Piperidinone)

  Mrv1652305261923552D          

  7  7  0  0  0  0            999 V2000
   10.8728   -8.8558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0479   -8.8558    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2853   -9.5703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6355   -9.5703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8728  -10.2848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0479  -10.2848    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.2853  -10.9994    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0011749

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H9NO/c7-5-3-1-2-4-6-5/h1-4H2,(H,6,7)

> <INCHI_KEY>
XUWHAWMETYGRKB-UHFFFAOYSA-N

> <FORMULA>
C5H9NO

> <MOLECULAR_WEIGHT>
99.1311

> <EXACT_MASS>
99.068413915

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.662282901878665

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperidin-2-one

> <ALOGPS_LOGP>
-0.40

> <JCHEM_LOGP>
-0.1350406333333333

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.88923083444066

> <JCHEM_PKA_STRONGEST_BASIC>
-1.61365657284703

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
26.858900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.29e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
delta-valerolactam

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0011749 (2-Piperidinone)

HMDB0011749
     RDKit          3D
2-Piperidinone
 16 16  0  0  0  0  0  0  0  0999 V2000
    2.3868    1.4900   -0.1212 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3294    0.8149   -0.0955 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0158    1.4295   -0.2280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9563    0.6031    0.6451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0679   -0.7574    0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2480   -1.3887   -0.3021 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3874   -0.6023    0.0662 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0533    2.4729    0.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3227    1.3469   -1.2763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5817    0.5618    1.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9378    1.1089    0.5985 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7363   -1.4074    0.6351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6039   -0.5895   -0.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.6214   -1.3969 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3191   -2.3881    0.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2480   -1.0731    0.4489 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  7  1  0
  7  2  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
  7 16  1  0
M  END
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PDB for HMDB0011749 (2-Piperidinone)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      20.296 -16.531   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      18.756 -16.531   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.066 -17.865   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      17.986 -17.865   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.296 -19.198   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      18.756 -19.198   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0      21.066 -20.532   0.000  0.00  0.00           O+0
CONECT    1    3    2                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7    6                                                  
CONECT    6    4    5                                                       
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0011749 (2-Piperidinone)

COMPND    HMDB0011749
HETATM    1  O1  UNL     1       2.387   1.490  -0.121  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.329   0.815  -0.095  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.016   1.430  -0.228  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.956   0.603   0.645  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.068  -0.757   0.003  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.248  -1.389  -0.302  1.00  0.00           C  
HETATM    7  N1  UNL     1       1.387  -0.602   0.066  1.00  0.00           N  
HETATM    8  H1  UNL     1      -0.053   2.473   0.131  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.323   1.347  -1.276  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.582   0.562   1.668  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.938   1.109   0.598  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.736  -1.407   0.635  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.604  -0.590  -0.977  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.357  -1.621  -1.397  1.00  0.00           H  
HETATM   15  H8  UNL     1       0.319  -2.388   0.201  1.00  0.00           H  
HETATM   16  H9  UNL     1       2.248  -1.073   0.449  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5   10   11
CONECT    5    6   12   13
CONECT    6    7   14   15
CONECT    7   16
END
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SMILES for HMDB0011749 (2-Piperidinone)

O=C1CCCCN1
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INCHI for HMDB0011749 (2-Piperidinone)

InChI=1S/C5H9NO/c7-5-3-1-2-4-6-5/h1-4H2,(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H9NO
Average Molecular Weight99.1311
Monoisotopic Molecular Weight99.068413915
IUPAC Namepiperidin-2-one
Traditional Namedelta-valerolactam
CAS Registry Number675-20-7
SMILES
O=C1CCCCN1
InChI Identifier
InChI=1S/C5H9NO/c7-5-3-1-2-4-6-5/h1-4H2,(H,6,7)
InChI KeyXUWHAWMETYGRKB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidinones. Piperidinones are compounds containing a piperidine ring which bears a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPiperidines
Sub ClassPiperidinones
Direct ParentPiperidinones
Alternative Parents
Substituents
  • Delta-lactam
  • Piperidinone
  • Secondary carboxylic acid amide
  • Lactam
  • Carboxamide group
  • Azacycle
  • Carboxylic acid derivative
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Carbonyl group
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point39.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility291 mg/mL at 25 °CNot Available
LogP-0.46HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
    • Zerihun T. Dame, ...
 details
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Ovarian cancer
  1. Zhang T, Wu X, Yin M, Fan L, Zhang H, Zhao F, Zhang W, Ke C, Zhang G, Hou Y, Zhou X, Lou G, Li K: Discrimination between malignant and benign ovarian tumors by plasma metabolomic profiling using ultra performance liquid chromatography/mass spectrometry. Clin Chim Acta. 2012 May 18;413(9-10):861-8. doi: 10.1016/j.cca.2012.01.026. Epub 2012 Jan 30. [PubMed:22309680 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello Bde L, Ratcliffe NM, Probert CS: An investigation of fecal volatile organic metabolites in irritable bowel syndrome. PLoS One. 2013;8(3):e58204. doi: 10.1371/journal.pone.0058204. Epub 2013 Mar 13. [PubMed:23516449 ]
  2. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Ulcerative colitis
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
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 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028421
KNApSAcK IDC00052660
Chemspider ID12144
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link2-Piperidinone
METLIN IDNot Available
PubChem Compound12665
PDB IDNot Available
ChEBI ID77761
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1234601
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available