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Showing metabocard for 5,6-Dichloro-1H-benzimidazole (HMDB0247168)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:10:53 UTC
Update Date2021-09-26 22:56:40 UTC
HMDB IDHMDB0247168
Secondary Accession NumbersNone
Metabolite Identification
Common Name5,6-Dichloro-1H-benzimidazole
Description5,6-dichloro-1H-1,3-benzodiazole belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds). Based on a literature review a small amount of articles have been published on 5,6-dichloro-1H-1,3-benzodiazole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5,6-dichloro-1h-benzimidazole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5,6-Dichloro-1H-benzimidazole 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 HMDB0247168 (5,6-Dichloro-1H-benzimidazole)


  Mrv1652309112102112D          

 11 12  0  0  0  0            999 V2000
    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 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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 N   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
  5  8  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
M  END
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3D MOL for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

HMDB0247168
     RDKit          3D
5,6-Dichloro-1H-benzimidazole
 15 16  0  0  0  0  0  0  0  0999 V2000
    3.6350   -1.0287   -0.0809 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.9815   -0.4796   -0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9194   -1.3733    0.0314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3847   -0.9191    0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5931   -1.5048    0.1266 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720   -0.5860    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9584    0.6021    0.0414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6245    0.4344    0.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4536    1.3230   -0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7582    0.8799   -0.1033 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1122    2.0137   -0.2041 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.0986   -2.4473    0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6312   -0.8165    0.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4270    1.5279    0.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2324    2.3743   -0.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  8  4  2  0
  3 12  1  0
  6 13  1  0
  7 14  1  0
  9 15  1  0
M  END
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3D SDF for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)


  Mrv1652309112102112D          

 11 12  0  0  0  0            999 V2000
    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 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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 N   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
  5  8  1  0  0  0  0
  3  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
  2 11  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0247168

> <DATABASE_NAME>
hmdb

> <SMILES>
ClC1=C(Cl)C=C2N=CNC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H4Cl2N2/c8-4-1-6-7(2-5(4)9)11-3-10-6/h1-3H,(H,10,11)

> <INCHI_KEY>
IPRDZAMUYMOJTA-UHFFFAOYSA-N

> <FORMULA>
C7H4Cl2N2

> <MOLECULAR_WEIGHT>
187.02

> <EXACT_MASS>
185.9751535

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
16.69287953966584

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,6-dichloro-1H-1,3-benzodiazole

> <ALOGPS_LOGP>
2.72

> <JCHEM_LOGP>
2.4675933516666664

> <ALOGPS_LOGS>
-2.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.92537693355845

> <JCHEM_PKA_STRONGEST_BASIC>
5.662405944978685

> <JCHEM_POLAR_SURFACE_AREA>
28.68

> <JCHEM_REFRACTIVITY>
44.57809999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.98e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5,6-dichloro-1H-1,3-benzodiazole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

HMDB0247168
     RDKit          3D
5,6-Dichloro-1H-benzimidazole
 15 16  0  0  0  0  0  0  0  0999 V2000
    3.6350   -1.0287   -0.0809 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.9815   -0.4796   -0.0479 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9194   -1.3733    0.0314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3847   -0.9191    0.0564 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5931   -1.5048    0.1266 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5720   -0.5860    0.1185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9584    0.6021    0.0414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6245    0.4344    0.0019 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4536    1.3230   -0.0777 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7582    0.8799   -0.1033 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1122    2.0137   -0.2041 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.0986   -2.4473    0.0751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6312   -0.8165    0.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4270    1.5279    0.0149 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2324    2.3743   -0.1188 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  2  1  0
  8  4  2  0
  3 12  1  0
  6 13  1  0
  7 14  1  0
  9 15  1  0
M  END
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PDB for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000  -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       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7 Cl   UNK     0       4.001  -0.770   0.000  0.00  0.00          Cl+0
HETATM    8 Cl   UNK     0       4.001   2.310   0.000  0.00  0.00          Cl+0
HETATM    9  N   UNK     0      -1.465   2.016   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      -1.465  -0.476   0.000  0.00  0.00           N+0
CONECT    1    2    6                                                       
CONECT    2    1    3   11                                                  
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    3   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    2                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   24    0
END
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3D PDB for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

COMPND    HMDB0247168
HETATM    1 CL1  UNL     1       3.635  -1.029  -0.081  1.00  0.00          CL  
HETATM    2  C1  UNL     1       1.981  -0.480  -0.048  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.919  -1.373   0.031  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.385  -0.919   0.056  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.593  -1.505   0.127  1.00  0.00           N  
HETATM    6  C4  UNL     1      -2.572  -0.586   0.118  1.00  0.00           C  
HETATM    7  N2  UNL     1      -1.958   0.602   0.041  1.00  0.00           N  
HETATM    8  C5  UNL     1      -0.625   0.434   0.002  1.00  0.00           C  
HETATM    9  C6  UNL     1       0.454   1.323  -0.078  1.00  0.00           C  
HETATM   10  C7  UNL     1       1.758   0.880  -0.103  1.00  0.00           C  
HETATM   11 CL2  UNL     1       3.112   2.014  -0.204  1.00  0.00          CL  
HETATM   12  H1  UNL     1       1.099  -2.447   0.075  1.00  0.00           H  
HETATM   13  H2  UNL     1      -3.631  -0.816   0.167  1.00  0.00           H  
HETATM   14  H3  UNL     1      -2.427   1.528   0.015  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.232   2.374  -0.119  1.00  0.00           H  
CONECT    1    2
CONECT    2    3    3   10
CONECT    3    4   12
CONECT    4    5    8    8
CONECT    5    6    6
CONECT    6    7   13
CONECT    7    8   14
CONECT    8    9
CONECT    9   10   10   15
CONECT   10   11
END
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SMILES for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

ClC1=C(Cl)C=C2N=CNC2=C1
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INCHI for HMDB0247168 (5,6-Dichloro-1H-benzimidazole)

InChI=1S/C7H4Cl2N2/c8-4-1-6-7(2-5(4)9)11-3-10-6/h1-3H,(H,10,11)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5,6-Dichloro-1--beta-D-benzimidazoleMeSH
5,6-DichlorobenzimidazoleMeSH
Chemical FormulaC7H4Cl2N2
Average Molecular Weight187.02
Monoisotopic Molecular Weight185.9751535
IUPAC Name5,6-dichloro-1H-1,3-benzodiazole
Traditional Name5,6-dichloro-1H-1,3-benzodiazole
CAS Registry NumberNot Available
SMILES
ClC1=C(Cl)C=C2N=CNC2=C1
InChI Identifier
InChI=1S/C7H4Cl2N2/c8-4-1-6-7(2-5(4)9)11-3-10-6/h1-3H,(H,10,11)
InChI KeyIPRDZAMUYMOJTA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as benzimidazoles. These are organic compounds containing a benzene ring fused to an imidazole ring (five member ring containing a nitrogen atom, 4 carbon atoms, and two double bonds).
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzimidazoles
Sub ClassNot Available
Direct ParentBenzimidazoles
Alternative Parents
Substituents
  • Benzimidazole
  • Benzenoid
  • Aryl halide
  • Aryl chloride
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organochloride
  • Organohalogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP2.72ALOGPS
logP2.47ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)11.93ChemAxon
pKa (Strongest Basic)5.66ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity44.58 m³·mol⁻¹ChemAxon
Polarizability16.69 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+134.92430932474
DeepCCS[M-H]-131.4930932474
DeepCCS[M-2H]-168.50130932474
DeepCCS[M+Na]+144.0230932474
AllCCS[M+H]+134.932859911
AllCCS[M+H-H2O]+130.532859911
AllCCS[M+NH4]+139.132859911
AllCCS[M+Na]+140.332859911
AllCCS[M-H]-126.932859911
AllCCS[M+Na-2H]-127.732859911
AllCCS[M+HCOO]-128.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5,6-Dichloro-1H-benzimidazoleClC1=C(Cl)C=C2N=CNC2=C12515.5Standard polar33892256
5,6-Dichloro-1H-benzimidazoleClC1=C(Cl)C=C2N=CNC2=C11666.6Standard non polar33892256
5,6-Dichloro-1H-benzimidazoleClC1=C(Cl)C=C2N=CNC2=C11977.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5,6-Dichloro-1H-benzimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C211959.9Semi standard non polar33892256
5,6-Dichloro-1H-benzimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C211837.4Standard non polar33892256
5,6-Dichloro-1H-benzimidazole,1TMS,isomer #1C[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C212192.0Standard polar33892256
5,6-Dichloro-1H-benzimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C212190.1Semi standard non polar33892256
5,6-Dichloro-1H-benzimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C212019.5Standard non polar33892256
5,6-Dichloro-1H-benzimidazole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=NC2=CC(Cl)=C(Cl)C=C212276.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dichloro-1H-benzimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-000i-0900000000-ca318f17ba713423a7d82021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5,6-Dichloro-1H-benzimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 10V, Positive-QTOFsplash10-000i-0900000000-2e9a77b9a18fab35f65c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 20V, Positive-QTOFsplash10-000i-0900000000-2e9a77b9a18fab35f65c2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 40V, Positive-QTOFsplash10-000i-0900000000-7e1ebd21a4fc414f4ab22021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 10V, Negative-QTOFsplash10-001i-0900000000-1a49d256a0d35835cf032021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 20V, Negative-QTOFsplash10-001i-0900000000-1a49d256a0d35835cf032021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5,6-Dichloro-1H-benzimidazole 40V, Negative-QTOFsplash10-001i-0900000000-1a49d256a0d35835cf032021-10-12Wishart LabView Spectrum
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 ID293966
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound331775
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 ]