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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 23:10:43 UTC

Update Date

2021-09-26 22:55:01 UTC

HMDB ID

HMDB0246142

Secondary Accession Numbers

None

Metabolite Identification

Common Name

2-Chloro-5-nitro-N-4-pyridinylbenzamide

Description

2-Chloro-5-nitro-N-4-pyridinylbenzamide belongs to the class of organic compounds known as 2-halobenzoic acids and derivatives. These are benzoic acids or derivatives carrying a halogen atom at the 2-position of the benzene ring. Based on a literature review a small amount of articles have been published on 2-Chloro-5-nitro-N-4-pyridinylbenzamide. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-chloro-5-nitro-n-4-pyridinylbenzamide is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Chloro-5-nitro-N-4-pyridinylbenzamide 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

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309112101102D          

 19 20  0  0  0  0            999 V2000
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    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
  4 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
  3 19  1  0  0  0  0
M  CHG  2   7   1   9  -1
M  END
> <DATABASE_ID>
HMDB0246142

> <DATABASE_NAME>
hmdb

> <SMILES>
[O-][N+](=O)C1=CC(C(=O)NC2=CC=NC=C2)=C(Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H8ClN3O3/c13-11-2-1-9(16(18)19)7-10(11)12(17)15-8-3-5-14-6-4-8/h1-7H,(H,14,15,17)

> <INCHI_KEY>
FRPJSHKMZHWJBE-UHFFFAOYSA-N

> <FORMULA>
C12H8ClN3O3

> <MOLECULAR_WEIGHT>
277.66

> <EXACT_MASS>
277.0254188

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
25.481703862382297

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-chloro-5-nitro-N-(pyridin-4-yl)benzamide

> <ALOGPS_LOGP>
2.50

> <JCHEM_LOGP>
2.3914870603333336

> <ALOGPS_LOGS>
-3.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.365898218658687

> <JCHEM_PKA_STRONGEST_BASIC>
5.6125325402343815

> <JCHEM_POLAR_SURFACE_AREA>
85.13

> <JCHEM_REFRACTIVITY>
70.5599

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.09e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-chloro-5-nitro-N-(pyridin-4-yl)benzamide

> <JCHEM_VEBER_RULE>
0

$$$$

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       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       2.667  -3.080   0.000  0.00  0.00           N+1
HETATM    8  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O-1
HETATM   10  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0       0.000  -9.240   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0      -4.001 -11.550   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   19 Cl   UNK     0       2.667  -9.240   0.000  0.00  0.00          Cl+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   19                                                  
CONECT    4    3    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    4   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13                                                       
CONECT   19    3                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

COMPND    HMDB0246142
HETATM    1  O1  UNL     1      -0.403   1.064   1.604  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.124   0.537   0.517  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.094  -0.115  -0.253  1.00  0.00           N  
HETATM    4  C2  UNL     1      -2.449  -0.259   0.076  1.00  0.00           C  
HETATM    5  C3  UNL     1      -3.073   0.206   1.207  1.00  0.00           C  
HETATM    6  C4  UNL     1      -4.434  -0.013   1.398  1.00  0.00           C  
HETATM    7  N2  UNL     1      -5.169  -0.670   0.506  1.00  0.00           N  
HETATM    8  C5  UNL     1      -4.584  -1.135  -0.607  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.250  -0.945  -0.840  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.280   0.620   0.058  1.00  0.00           C  
HETATM   11  C8  UNL     1       2.172  -0.365   0.406  1.00  0.00           C  
HETATM   12  C9  UNL     1       3.492  -0.347   0.011  1.00  0.00           C  
HETATM   13  N3  UNL     1       4.367  -1.396   0.403  1.00  0.00           N1+
HETATM   14  O2  UNL     1       3.947  -2.335   1.104  1.00  0.00           O  
HETATM   15  O3  UNL     1       5.690  -1.426   0.037  1.00  0.00           O1-
HETATM   16  C10 UNL     1       3.960   0.693  -0.766  1.00  0.00           C  
HETATM   17  C11 UNL     1       3.069   1.684  -1.117  1.00  0.00           C  
HETATM   18  C12 UNL     1       1.743   1.656  -0.715  1.00  0.00           C  
HETATM   19 CL1  UNL     1       0.653   2.956  -1.199  1.00  0.00          CL  
HETATM   20  H1  UNL     1      -0.746  -0.536  -1.174  1.00  0.00           H  
HETATM   21  H2  UNL     1      -2.517   0.735   1.939  1.00  0.00           H  
HETATM   22  H3  UNL     1      -4.875   0.382   2.319  1.00  0.00           H  
HETATM   23  H4  UNL     1      -5.155  -1.678  -1.358  1.00  0.00           H  
HETATM   24  H5  UNL     1      -2.804  -1.334  -1.753  1.00  0.00           H  
HETATM   25  H6  UNL     1       1.835  -1.203   1.020  1.00  0.00           H  
HETATM   26  H7  UNL     1       5.004   0.732  -1.092  1.00  0.00           H  
HETATM   27  H8  UNL     1       3.464   2.493  -1.730  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   20
CONECT    4    5    5    9
CONECT    5    6   21
CONECT    6    7    7   22
CONECT    7    8
CONECT    8    9    9   23
CONECT    9   24
CONECT   10   11   11   18
CONECT   11   12   25
CONECT   12   13   16   16
CONECT   13   14   14   15
CONECT   16   17   26
CONECT   17   18   18   27
CONECT   18   19
END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₂H₈ClN₃O₃

Average Molecular Weight

277.66

Monoisotopic Molecular Weight

277.0254188

IUPAC Name

2-chloro-5-nitro-N-(pyridin-4-yl)benzamide

Traditional Name

2-chloro-5-nitro-N-(pyridin-4-yl)benzamide

CAS Registry Number

Not Available

SMILES

[O-][N+](=O)C1=CC(C(=O)NC2=CC=NC=C2)=C(Cl)C=C1

InChI Identifier

InChI=1S/C12H8ClN3O3/c13-11-2-1-9(16(18)19)7-10(11)12(17)15-8-3-5-14-6-4-8/h1-7H,(H,14,15,17)

InChI Key

FRPJSHKMZHWJBE-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2-halobenzoic acids and derivatives. These are benzoic acids or derivatives carrying a halogen atom at the 2-position of the benzene ring.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

2-halobenzoic acids and derivatives

Alternative Parents

Substituents

2-halobenzoic acid or derivatives
Benzamide
Nitrobenzene
Nitroaromatic compound
Benzoyl
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Pyridine
Heteroaromatic compound
Vinylogous halide
Carboxamide group
C-nitro compound
Organic nitro compound
Secondary carboxylic acid amide
Propargyl-type 1,3-dipolar organic compound
Organoheterocyclic compound
Allyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Carboxylic acid derivative
Organic oxoazanium
Azacycle
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organohalogen compound
Hydrocarbon derivative
Organochloride
Organic oxide
Organonitrogen compound
Organic zwitterion
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.5	ALOGPS
logP	2.39	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	10.37	ChemAxon
pKa (Strongest Basic)	5.61	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	85.13 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	70.56 m³·mol⁻¹	ChemAxon
Polarizability	25.48 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	156.016	30932474
DeepCCS	[M-H]-	153.62	30932474
DeepCCS	[M-2H]-	187.287	30932474
DeepCCS	[M+Na]+	162.459	30932474
AllCCS	[M+H]+	158.4	32859911
AllCCS	[M+H-H2O]+	154.8	32859911
AllCCS	[M+NH4]+	161.9	32859911
AllCCS	[M+Na]+	162.8	32859911
AllCCS	[M-H]-	156.6	32859911
AllCCS	[M+Na-2H]-	156.1	32859911
AllCCS	[M+HCOO]-	155.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-5-nitro-N-4-pyridinylbenzamide	[O-][N+](=O)C1=CC(C(=O)NC2=CC=NC=C2)=C(Cl)C=C1	3751.3	Standard polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide	[O-][N+](=O)C1=CC(C(=O)NC2=CC=NC=C2)=C(Cl)C=C1	2518.3	Standard non polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide	[O-][N+](=O)C1=CC(C(=O)NC2=CC=NC=C2)=C(Cl)C=C1	2609.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TMS,isomer #1	C[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	2320.4	Semi standard non polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TMS,isomer #1	C[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	2371.8	Standard non polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TMS,isomer #1	C[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	3225.7	Standard polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	2608.2	Semi standard non polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	2558.1	Standard non polar	33892256
2-Chloro-5-nitro-N-4-pyridinylbenzamide,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(C(=O)C1=CC([N+](=O)[O-])=CC=C1Cl)C1=CC=NC=C1	3264.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-5-nitro-N-4-pyridinylbenzamide GC-MS (Non-derivatized) - 70eV, Positive	splash10-05di-9670000000-502416db41331df11fdf	2021-09-23	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2-Chloro-5-nitro-N-4-pyridinylbenzamide GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

2057673

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

2777391

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]

Showing metabocard for 2-Chloro-5-nitro-N-4-pyridinylbenzamide (HMDB0246142)

MOL for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

3D MOL for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

3D SDF for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

3D-SDF for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

PDB for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

3D PDB for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

SMILES for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

INCHI for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

Structure for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

3D Structure for HMDB0246142 (2-Chloro-5-nitro-N-4-pyridinylbenzamide)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra