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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (6) Show 6 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 21:04:09 UTC

Update Date

2021-10-01 18:39:41 UTC

HMDB ID

HMDB0243844

Secondary Accession Numbers

None

Metabolite Identification

Common Name

1-Chloro-2,4-dinitrobenzene

Description

1-Chloro-2,4-dinitrobenzene, also known as 2,4-dinitrochlorobenzene or 2,4-dinitrophenyl chloride, belongs to the class of organic compounds known as nitrobenzenes. Nitrobenzenes are compounds containing a nitrobenzene moiety, which consists of a benzene ring with a carbon bearing a nitro group. 1-Chloro-2,4-dinitrobenzene exists in all living organisms, ranging from bacteria to humans. 1-Chloro-2,4-dinitrobenzene has been detected, but not quantified in, several different foods, such as pecan nuts (Carya illinoinensis), almonds (Prunus dulcis), white cabbages (Brassica oleracea L. var. capitata L. f. alba DC.), canada blueberries (Vaccinium myrtilloides), and pepper (c. baccatum). This could make 1-chloro-2,4-dinitrobenzene a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on 1-Chloro-2,4-dinitrobenzene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1-chloro-2,4-dinitrobenzene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1-Chloro-2,4-dinitrobenzene 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

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         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       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7 Cl   UNK     0       1.334  -2.310   0.000  0.00  0.00          Cl+0
HETATM    8  N   UNK     0       1.334   3.850   0.000  0.00  0.00           N+0
HETATM    9  N   UNK     0      -1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    4                                                       
CONECT    2    1    5                                                       
CONECT    3    4    6                                                       
CONECT    4    1    3    8                                                  
CONECT    5    2    6    7                                                  
CONECT    6    3    5    9                                                  
CONECT    7    5                                                            
CONECT    8    4   10   11                                                  
CONECT    9    6   12   13                                                  
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,3-Dinitro-4-chlorobenzene	ChEBI
1-Chloro-2,4-dinitrobenzol	ChEBI
2,4-Dinitro-1-chlorobenzene	ChEBI
2,4-Dinitrochlorobenzene	ChEBI
2,4-Dinitrophenyl chloride	ChEBI
4-Chloro-1,3-dinitrobenzene	ChEBI
6-Chloro-1,3-dinitrobenzene	ChEBI
CDNB	ChEBI
Chlorodinitrobenzene	ChEBI
CLDNB	ChEBI
Dinitrochlorobenzene	ChEBI
DNCB	ChEBI
DNPCL	ChEBI
1 Chloro 2,4 dinitrobenzene	HMDB
1-Chloro-2,4-dinitrobenzene	KEGG

Chemical Formula

C₆H₃ClN₂O₄

Average Molecular Weight

202.552

Monoisotopic Molecular Weight

201.978134301

IUPAC Name

1-chloro-2,4-dinitrobenzene

Traditional Name

Cdnb

CAS Registry Number

Not Available

SMILES

ClC1=C(C=C(C=C1)N(=O)=O)N(=O)=O

InChI Identifier

InChI=1S/C6H3ClN2O4/c7-5-2-1-4(8(10)11)3-6(5)9(12)13/h1-3H

InChI Key

VYZAHLCBVHPDDF-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nitrobenzenes. Nitrobenzenes are compounds containing a nitrobenzene moiety, which consists of a benzene ring with a carbon bearing a nitro group.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Nitrobenzenes

Direct Parent

Nitrobenzenes

Alternative Parents

Substituents

Nitrobenzene
Nitroaromatic compound
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
C-nitro compound
Organic nitro compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Allyl-type 1,3-dipolar organic compound
Organic oxoazanium
Organic nitrogen compound
Organochloride
Organohalogen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

C-nitro compound (CHEBI:34718 )
monochlorobenzenes (CHEBI:34718 )
a small molecule (1-CHLORO-24-DINITROBENZENE )

Ontology

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	2.29	ALOGPS
logP	2.46	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	19.94	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	91.64 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	45.51 m³·mol⁻¹	ChemAxon
Polarizability	15.73 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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]+	138.056	30932474
DeepCCS	[M-H]-	135.661	30932474
DeepCCS	[M-2H]-	170.582	30932474
DeepCCS	[M+Na]+	146.121	30932474
AllCCS	[M+H]+	137.3	32859911
AllCCS	[M+H-H2O]+	133.2	32859911
AllCCS	[M+NH4]+	141.2	32859911
AllCCS	[M+Na]+	142.3	32859911
AllCCS	[M-H]-	126.8	32859911
AllCCS	[M+Na-2H]-	127.2	32859911
AllCCS	[M+HCOO]-	127.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022.	4.91 minutes	32390414
Predicted by Siyang on May 30, 2022	16.834 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.74 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1871.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	650.5 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	233.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	452.5 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	330.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	626.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	695.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	685.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	1418.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	546.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1322.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	567.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	434.5 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	692.2 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	580.3 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	136.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
1-Chloro-2,4-dinitrobenzene	ClC1=C(C=C(C=C1)N(=O)=O)N(=O)=O	2566.7	Standard polar	33892256
1-Chloro-2,4-dinitrobenzene	ClC1=C(C=C(C=C1)N(=O)=O)N(=O)=O	1465.6	Standard non polar	33892256
1-Chloro-2,4-dinitrobenzene	ClC1=C(C=C(C=C1)N(=O)=O)N(=O)=O	1542.7	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - 1-Chloro-2,4-dinitrobenzene EI-B (Non-derivatized)	splash10-0w59-9530000000-7ea2caea63400fe591c1	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Chloro-2,4-dinitrobenzene GC-MS (Non-derivatized) - 70eV, Positive	splash10-0uk9-8790000000-32f6280952e44abd2d1c	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 1-Chloro-2,4-dinitrobenzene GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
MS	Mass Spectrum (Electron Ionization)	splash10-0gz9-9420000000-4d294e9fc091f8cae0d6	2014-10-20	Not Available	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene APCI-ITFT , negative-QTOF	splash10-00di-0900000000-85303c0c3a1f120d7a74	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 10V, Positive-QTOF	splash10-0udi-0090000000-c573b491328121e4cf78	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 20V, Positive-QTOF	splash10-004j-0900000000-1c001a7036c618057ee9	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 40V, Positive-QTOF	splash10-002b-0900000000-43bebc40ccd73ff3c89a	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 10V, Negative-QTOF	splash10-0udi-0290000000-d1014832aa18469c9675	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 20V, Negative-QTOF	splash10-0udi-0190000000-b66c9114d7746ef2f38a	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 1-Chloro-2,4-dinitrobenzene 40V, Negative-QTOF	splash10-0fbc-1910000000-a88b7ac767e570299431	2016-08-03	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View

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

DB11831

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030243

KNApSAcK ID

Not Available

Chemspider ID

13868426

KEGG Compound ID

C14397

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

2,4-Dinitrochlorobenzene

METLIN ID

Not Available

PubChem Compound

PDB ID

Not Available

ChEBI ID

34718

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1252731

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 ]

Enzymes

Enzyme Details

1. Prostaglandin E synthase

General function:: Involved in prostaglandin-E synthase activity
Specific function:: Catalyzes the oxidoreduction of prostaglandin endoperoxide H2 (PGH2) to prostaglandin E2 (PGE2).
Gene Name:: PTGES
Uniprot ID:: O14684
Molecular weight:: 17102.135

Enzyme Details

2. Glutathione S-transferase kappa 1

General function:: Involved in protein disulfide oxidoreductase activity
Specific function:: Significant glutathione conjugating activity is found only with the model substrate, 1-chloro-2,4-dinitrobenzene (CDNB).
Gene Name:: GSTK1
Uniprot ID:: Q9Y2Q3
Molecular weight:: 31565.605

Enzyme Details

3. Glutathione S-transferase Mu 4

General function:: Involved in glutathione transferase activity
Specific function:: Conjugation of reduced glutathione to a wide number of exogenous and endogenous hydrophobic electrophiles. Active on 1-chloro-2,4-dinitrobenzene.
Gene Name:: GSTM4
Uniprot ID:: Q03013
Molecular weight:: 25561.095

Enzyme Details

4. Microsomal glutathione S-transferase 2

General function:: Involved in enzyme activator activity
Specific function:: Can catalyze the production of LTC4 from LTA4 and reduced glutathione. Can catalyze the conjugation of 1-chloro-2,4-dinitrobenzene with reduced glutathione.
Gene Name:: MGST2
Uniprot ID:: Q99735
Molecular weight:: 16620.4

Enzyme Details

5. Glutathione S-transferase LANCL1

General function:: Not Available
Specific function:: Functions as glutathione transferase. Catalyzes conjugation of the glutathione (GSH) to artificial substrates 1-chloro-2,4-dinitrobenzene (CDNB) and p-nitrophenyl acetate. Mitigates neuronal oxidative stress during normal postnatal development and in response to oxidative stresses probably through GSH antioxidant defense mechanism (By similarity). May play a role in EPS8 signaling. Binds glutathione (PubMed:19528316).
Gene Name:: LANCL1
Uniprot ID:: O43813
Molecular weight:: 45282.71

Enzyme Details

6. Glutathione S-transferase LANCL1

General function:: Not Available
Specific function:: Functions as glutathione transferase (PubMed:25158856). Catalyzes conjugation of the glutathione (GSH) to artificial substrates 1-chloro-2,4-dinitrobenzene (CDNB) and p-nitrophenyl acetate (PubMed:25158856). Mitigates neuronal oxidative stress during normal postnatal development and in response to oxidative stresses probably through GSH antioxidant defense mechanism (PubMed:25158856). May play a role in EPS8 signaling. Binds glutathione (By similarity).
Gene Name:: LANCL1
Uniprot ID:: O89112
Molecular weight:: 45340.74

Showing metabocard for 1-Chloro-2,4-dinitrobenzene (HMDB0243844)

MOL for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

3D MOL for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

3D SDF for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

3D-SDF for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

PDB for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

3D PDB for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

SMILES for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

INCHI for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

Structure for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

3D Structure for HMDB0243844 (1-Chloro-2,4-dinitrobenzene)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes