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Showing metabocard for 6-Chloronicotinic acid (HMDB0247049)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:04:00 UTC
Update Date2021-09-26 22:56:30 UTC
HMDB IDHMDB0247049
Secondary Accession NumbersNone
Metabolite Identification
Common Name6-Chloronicotinic acid
Description6-Chloronicotinic acid belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group. Based on a literature review a significant number of articles have been published on 6-Chloronicotinic acid. This compound has been identified in human blood as reported by (PMID: 31557052 ). 6-chloronicotinic acid is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 6-Chloronicotinic 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 HMDB0247049 (6-Chloronicotinic acid)


  Mrv1652309112102042D          

 10 10  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
    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 N   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
    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
    0.7145   -1.2375    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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0247049 (6-Chloronicotinic acid)

HMDB0247049
     RDKit          3D
6-Chloronicotinic acid
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.5878   -1.5680    0.0027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0191   -0.4584    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7889    0.6773    0.3127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5577   -0.3427    0.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0598    0.8703    0.1470 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4359    0.9597    0.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2002   -0.1686   -0.1338 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9371    0.0257   -0.2247 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5874   -1.3618   -0.2502 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2297   -1.4567   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5695    1.5818   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5702    1.7445    0.3047 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9220    1.9045    0.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2788   -2.4075   -0.2631 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
 10 14  1  0
M  END
Download

3D SDF for HMDB0247049 (6-Chloronicotinic acid)


  Mrv1652309112102042D          

 10 10  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
    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 N   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
    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
    0.7145   -1.2375    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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  3 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247049

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=CN=C(Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H4ClNO2/c7-5-2-1-4(3-8-5)6(9)10/h1-3H,(H,9,10)

> <INCHI_KEY>
UAWMVMPAYRWUFX-UHFFFAOYSA-N

> <FORMULA>
C6H4ClNO2

> <MOLECULAR_WEIGHT>
157.55

> <EXACT_MASS>
156.9930561

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
13.627940160339024

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-chloropyridine-3-carboxylic acid

> <ALOGPS_LOGP>
0.70

> <JCHEM_LOGP>
1.2373781503333332

> <ALOGPS_LOGS>
-1.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7332117719822504

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6683044573170472

> <JCHEM_POLAR_SURFACE_AREA>
50.19

> <JCHEM_REFRACTIVITY>
37.02340000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.59e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-chloropyridine-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0247049 (6-Chloronicotinic acid)

HMDB0247049
     RDKit          3D
6-Chloronicotinic acid
 14 14  0  0  0  0  0  0  0  0999 V2000
   -2.5878   -1.5680    0.0027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0191   -0.4584    0.1110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7889    0.6773    0.3127 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5577   -0.3427    0.0283 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0598    0.8703    0.1470 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4359    0.9597    0.0665 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2002   -0.1686   -0.1338 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9371    0.0257   -0.2247 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.5874   -1.3618   -0.2502 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2297   -1.4567   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5695    1.5818   -0.0880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5702    1.7445    0.3047 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9220    1.9045    0.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2788   -2.4075   -0.2631 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  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  9  1  0
  9 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
 10 14  1  0
M  END
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PDB for HMDB0247049 (6-Chloronicotinic 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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0       0.000  -0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   2.310   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
HETATM   10 Cl   UNK     0       1.334  -2.310   0.000  0.00  0.00          Cl+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   10                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    3                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0247049 (6-Chloronicotinic acid)

COMPND    HMDB0247049
HETATM    1  O1  UNL     1      -2.588  -1.568   0.003  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.019  -0.458   0.111  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.789   0.677   0.313  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.558  -0.343   0.028  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.060   0.870   0.147  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.436   0.960   0.066  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.200  -0.169  -0.134  1.00  0.00           C  
HETATM    8 CL1  UNL     1       3.937   0.026  -0.225  1.00  0.00          CL  
HETATM    9  N1  UNL     1       1.587  -1.362  -0.250  1.00  0.00           N  
HETATM   10  C6  UNL     1       0.230  -1.457  -0.172  1.00  0.00           C  
HETATM   11  H1  UNL     1      -2.569   1.582  -0.088  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.570   1.745   0.305  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.922   1.905   0.159  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.279  -2.408  -0.263  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5    5   10
CONECT    5    6   12
CONECT    6    7    7   13
CONECT    7    8    9
CONECT    9   10   10
CONECT   10   14
END
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SMILES for HMDB0247049 (6-Chloronicotinic acid)

OC(=O)C1=CN=C(Cl)C=C1
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INCHI for HMDB0247049 (6-Chloronicotinic acid)

InChI=1S/C6H4ClNO2/c7-5-2-1-4(3-8-5)6(9)10/h1-3H,(H,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
6-ChloronicotinateGenerator
6-Chloropyridine-3-carboxylateHMDB
Chemical FormulaC6H4ClNO2
Average Molecular Weight157.55
Monoisotopic Molecular Weight156.9930561
IUPAC Name6-chloropyridine-3-carboxylic acid
Traditional Name6-chloropyridine-3-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=CN=C(Cl)C=C1
InChI Identifier
InChI=1S/C6H4ClNO2/c7-5-2-1-4(3-8-5)6(9)10/h1-3H,(H,9,10)
InChI KeyUAWMVMPAYRWUFX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyridinecarboxylic acids. Pyridinecarboxylic acids are compounds containing a pyridine ring bearing a carboxylic acid group.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyridines and derivatives
Sub ClassPyridinecarboxylic acids and derivatives
Direct ParentPyridinecarboxylic acids
Alternative Parents
Substituents
  • Pyridine carboxylic acid
  • 2-halopyridine
  • Aryl chloride
  • Aryl halide
  • Heteroaromatic compound
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • 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
PropertyValueSource
logP0.7ALOGPS
logP1.24ChemAxon
logS-1ALOGPS
pKa (Strongest Acidic)3.73ChemAxon
pKa (Strongest Basic)-0.67ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area50.19 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.02 m³·mol⁻¹ChemAxon
Polarizability13.63 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+130.39530932474
DeepCCS[M-H]-127.07930932474
DeepCCS[M-2H]-164.23130932474
DeepCCS[M+Na]+139.76530932474
AllCCS[M+H]+131.732859911
AllCCS[M+H-H2O]+127.132859911
AllCCS[M+NH4]+135.932859911
AllCCS[M+Na]+137.232859911
AllCCS[M-H]-126.932859911
AllCCS[M+Na-2H]-128.532859911
AllCCS[M+HCOO]-130.432859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202211.0271 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.84 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1347.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid391.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid122.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid264.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid96.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid369.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid467.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)241.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid798.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid307.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1063.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid285.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid358.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate620.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA364.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water239.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-Chloronicotinic acidOC(=O)C1=CN=C(Cl)C=C12249.4Standard polar33892256
6-Chloronicotinic acidOC(=O)C1=CN=C(Cl)C=C11438.2Standard non polar33892256
6-Chloronicotinic acidOC(=O)C1=CN=C(Cl)C=C11406.7Semi standard non polar33892256
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 ID71547
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNeonicotinoid
METLIN IDNot Available
PubChem Compound79222
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 ]