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Showing metabocard for Nipecotic acid (HMDB0255618)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 15:23:58 UTC
Update Date2021-09-26 23:10:36 UTC
HMDB IDHMDB0255618
Secondary Accession NumbersNone
Metabolite Identification
Common NameNipecotic acid
DescriptionNipecotic acid, also known as nipecotate, belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group. Based on a literature review a significant number of articles have been published on Nipecotic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). Nipecotic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Nipecotic acid 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 HMDB0255618 (Nipecotic acid)

  Mrv1652309112117242D          

  9  9  0  0  0  0            999 V2000
    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
    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 N   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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   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
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for HMDB0255618 (Nipecotic acid)

HMDB0255618
     RDKit          3D
Nipecotic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.4479   -0.5383    1.8497 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1868    0.0453    0.7736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2174    0.3586   -0.1039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8216    0.4323    0.3651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4072   -0.2281   -0.9457 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9394    0.2620   -1.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9453    0.3219   -0.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4396    0.7265    1.0157 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2195    0.0276    1.3829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0675    0.1120   -1.0742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7390    1.5433    0.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1271    0.0456   -1.7438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4373   -1.3328   -0.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3358   -0.4537   -2.1264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8086    1.2232   -1.8916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237   -0.6365   -0.2153 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7154    1.0911   -0.5605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1783    0.6489    1.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3960   -1.0648    1.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0497    0.2551    2.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 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
  7 17  1  0
  8 18  1  0
  9 19  1  0
  9 20  1  0
M  END
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3D SDF for HMDB0255618 (Nipecotic acid)

  Mrv1652309112117242D          

  9  9  0  0  0  0            999 V2000
    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
    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 N   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
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 O   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
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255618

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1CCCNC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c8-6(9)5-2-1-3-7-4-5/h5,7H,1-4H2,(H,8,9)

> <INCHI_KEY>
XJLSEXAGTJCILF-UHFFFAOYSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.159

> <EXACT_MASS>
129.078978598

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.479985373248663

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
piperidine-3-carboxylic acid

> <ALOGPS_LOGP>
-2.36

> <JCHEM_LOGP>
-2.435624186233799

> <ALOGPS_LOGS>
0.16

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.793972525745452

> <JCHEM_PKA_STRONGEST_BASIC>
10.240815714921297

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
32.921299999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.88e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
nipecotic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0255618 (Nipecotic acid)

HMDB0255618
     RDKit          3D
Nipecotic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.4479   -0.5383    1.8497 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1868    0.0453    0.7736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2174    0.3586   -0.1039 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8216    0.4323    0.3651 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4072   -0.2281   -0.9457 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9394    0.2620   -1.3494 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9453    0.3219   -0.2551 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4396    0.7265    1.0157 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2195    0.0276    1.3829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0675    0.1120   -1.0742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7390    1.5433    0.2509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1271    0.0456   -1.7438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4373   -1.3328   -0.7409 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3358   -0.4537   -2.1264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8086    1.2232   -1.8916 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5237   -0.6365   -0.2153 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7154    1.0911   -0.5605 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1783    0.6489    1.7219 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3960   -1.0648    1.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0497    0.2551    2.4117 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 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
  7 17  1  0
  8 18  1  0
  9 19  1  0
  9 20  1  0
M  END
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PDB for HMDB0255618 (Nipecotic acid)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   2.310   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  N   UNK     0       2.667   0.000   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0255618 (Nipecotic acid)

COMPND    HMDB0255618
HETATM    1  O1  UNL     1      -2.448  -0.538   1.850  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.187   0.045   0.774  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.217   0.359  -0.104  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.822   0.432   0.365  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.407  -0.228  -0.946  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.939   0.262  -1.349  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.945   0.322  -0.255  1.00  0.00           C  
HETATM    8  N1  UNL     1       1.440   0.727   1.016  1.00  0.00           N  
HETATM    9  C6  UNL     1       0.219   0.028   1.383  1.00  0.00           C  
HETATM   10  H1  UNL     1      -3.068   0.112  -1.074  1.00  0.00           H  
HETATM   11  H2  UNL     1      -0.739   1.543   0.251  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.127   0.046  -1.744  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.437  -1.333  -0.741  1.00  0.00           H  
HETATM   14  H5  UNL     1       1.336  -0.454  -2.126  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.809   1.223  -1.892  1.00  0.00           H  
HETATM   16  H7  UNL     1       2.524  -0.637  -0.215  1.00  0.00           H  
HETATM   17  H8  UNL     1       2.715   1.091  -0.561  1.00  0.00           H  
HETATM   18  H9  UNL     1       2.178   0.649   1.722  1.00  0.00           H  
HETATM   19  H10 UNL     1       0.396  -1.065   1.235  1.00  0.00           H  
HETATM   20  H11 UNL     1      -0.050   0.255   2.412  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    9   11
CONECT    5    6   12   13
CONECT    6    7   14   15
CONECT    7    8   16   17
CONECT    8    9   18
CONECT    9   19   20
END
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SMILES for HMDB0255618 (Nipecotic acid)

OC(=O)C1CCCNC1
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INCHI for HMDB0255618 (Nipecotic acid)

InChI=1S/C6H11NO2/c8-6(9)5-2-1-3-7-4-5/h5,7H,1-4H2,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
3-Piperidinecarboxylic acidChEBI
Hexahydronicotinic acidChEBI
Piperidine-3-carboxylic acidChEBI
3-PiperidinecarboxylateGenerator
HexahydronicotinateGenerator
Piperidine-3-carboxylateGenerator
NipecotateGenerator
(RS)-Nipecotic acidHMDB
Nipecotic acid hydrideHMDB
Nipecotic acid hydrochlorideHMDB
Nipecotic acid, (+-)-isomerHMDB
Nipecotic acid, (R)-isomerHMDB
Nipecotic acid, (S)-isomerHMDB
Chemical FormulaC6H11NO2
Average Molecular Weight129.159
Monoisotopic Molecular Weight129.078978598
IUPAC Namepiperidine-3-carboxylic acid
Traditional Namenipecotic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CCCNC1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-2-1-3-7-4-5/h5,7H,1-4H2,(H,8,9)
InChI KeyXJLSEXAGTJCILF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidinecarboxylic acids. Piperidinecarboxylic acids are compounds containing a piperidine ring which bears a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPiperidines
Sub ClassPiperidinecarboxylic acids and derivatives
Direct ParentPiperidinecarboxylic acids
Alternative Parents
Substituents
  • Piperidinecarboxylic acid
  • Amino acid or derivatives
  • Amino acid
  • Carboxylic acid derivative
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Secondary amine
  • Amine
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • 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
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
Predicted Chromatographic Properties
Spectra
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 ID4342
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNipecotic acid
METLIN IDNot Available
PubChem Compound4498
PDB IDNot Available
ChEBI ID116931
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 ]