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Showing metabocard for 3-(Chloromethyl)pyridine (HMDB0245786)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:50:19 UTC
Update Date2021-09-26 22:54:28 UTC
HMDB IDHMDB0245786
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-(Chloromethyl)pyridine
Description3-(Chloromethyl)pyridine, also known as 3-clmep, belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms. Based on a literature review a significant number of articles have been published on 3-(Chloromethyl)pyridine. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-(chloromethyl)pyridine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-(Chloromethyl)pyridine 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 HMDB0245786 (3-(Chloromethyl)pyridine)

  Mrv1652309112100502D          

  8  8  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 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for HMDB0245786 (3-(Chloromethyl)pyridine)

HMDB0245786
     RDKit          3D
3-(Chloromethyl)pyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.6960   -0.5919    1.4871 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0602    0.0974   -0.0469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    0.1508    0.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744   -0.9231   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5737   -0.9080   -0.4201 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2122    0.2097    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4617    1.2398    0.5010 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1244    1.2408    0.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4397   -0.4700   -0.8998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3914    1.1753   -0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -1.7805   -0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1278   -1.7668   -0.7802 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3003    0.2419    0.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4467    2.0846    0.8331 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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3D SDF for HMDB0245786 (3-(Chloromethyl)pyridine)

  Mrv1652309112100502D          

  8  8  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 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245786

> <DATABASE_NAME>
hmdb

> <SMILES>
ClCC1=CN=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H6ClN/c7-4-6-2-1-3-8-5-6/h1-3,5H,4H2

> <INCHI_KEY>
CNQCWYFDIQSALX-UHFFFAOYSA-N

> <FORMULA>
C6H6ClN

> <MOLECULAR_WEIGHT>
127.57

> <EXACT_MASS>
127.0188769

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
12.340698129184098

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-(chloromethyl)pyridine

> <ALOGPS_LOGP>
1.26

> <JCHEM_LOGP>
1.3428154776666665

> <ALOGPS_LOGS>
-0.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
4.81626421041204

> <JCHEM_POLAR_SURFACE_AREA>
12.89

> <JCHEM_REFRACTIVITY>
33.767999999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.12e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(chloromethyl)pyridine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0245786 (3-(Chloromethyl)pyridine)

HMDB0245786
     RDKit          3D
3-(Chloromethyl)pyridine
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.6960   -0.5919    1.4871 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -2.0602    0.0974   -0.0469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5697    0.1508    0.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744   -0.9231   -0.4492 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5737   -0.9080   -0.4201 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2122    0.2097    0.0705 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4617    1.2398    0.5010 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1244    1.2408    0.4798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4397   -0.4700   -0.8998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3914    1.1753   -0.0508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -1.7805   -0.8265 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1278   -1.7668   -0.7802 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3003    0.2419    0.1019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4467    2.0846    0.8331 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  3  1  0
  2  9  1  0
  2 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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PDB for HMDB0245786 (3-(Chloromethyl)pyridine)

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 Cl   UNK     0       0.000   4.620   0.000  0.00  0.00          Cl+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                                                       
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0245786 (3-(Chloromethyl)pyridine)

COMPND    HMDB0245786
HETATM    1 CL1  UNL     1      -2.696  -0.592   1.487  1.00  0.00          CL  
HETATM    2  C1  UNL     1      -2.060   0.097  -0.047  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.570   0.151   0.000  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.174  -0.923  -0.449  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.574  -0.908  -0.420  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.212   0.210   0.070  1.00  0.00           C  
HETATM    7  N1  UNL     1       1.462   1.240   0.501  1.00  0.00           N  
HETATM    8  C6  UNL     1       0.124   1.241   0.480  1.00  0.00           C  
HETATM    9  H1  UNL     1      -2.440  -0.470  -0.900  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.391   1.175  -0.051  1.00  0.00           H  
HETATM   11  H3  UNL     1      -0.371  -1.781  -0.826  1.00  0.00           H  
HETATM   12  H4  UNL     1       2.128  -1.767  -0.780  1.00  0.00           H  
HETATM   13  H5  UNL     1       3.300   0.242   0.102  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.447   2.085   0.833  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    9   10
CONECT    3    4    4    8
CONECT    4    5   11
CONECT    5    6    6   12
CONECT    6    7   13
CONECT    7    8    8
CONECT    8   14
END
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SMILES for HMDB0245786 (3-(Chloromethyl)pyridine)

ClCC1=CN=CC=C1
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INCHI for HMDB0245786 (3-(Chloromethyl)pyridine)

InChI=1S/C6H6ClN/c7-4-6-2-1-3-8-5-6/h1-3,5H,4H2
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Synonyms
ValueSource
3-(Chloromethyl)pyridine hydrochlorideHMDB
3-ClMePHMDB
Chemical FormulaC6H6ClN
Average Molecular Weight127.57
Monoisotopic Molecular Weight127.0188769
IUPAC Name3-(chloromethyl)pyridine
Traditional Name3-(chloromethyl)pyridine
CAS Registry NumberNot Available
SMILES
ClCC1=CN=CC=C1
InChI Identifier
InChI=1S/C6H6ClN/c7-4-6-2-1-3-8-5-6/h1-3,5H,4H2
InChI KeyCNQCWYFDIQSALX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridines and derivatives. Pyridines and derivatives are compounds containing a pyridine ring, which is a six-member aromatic heterocycle which consists of one nitrogen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassNot Available
Direct ParentPyridines and derivatives
Alternative Parents
Substituents
  • Pyridine
  • Heteroaromatic compound
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Alkyl halide
  • Alkyl chloride
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
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 ID17337
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound18358
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 ]