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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-08-13 03:39:40 UTC
Update Date2020-02-26 21:24:46 UTC
HMDB IDHMDB0003701
Secondary Accession Numbers
  • HMDB03701
Metabolite Identification
Common NameDimethylbenzimidazole
DescriptionDimethylbenzimidazole, also known as dimedazol, 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). Dimethylbenzimidazole exists in all living organisms, ranging from bacteria to humans. In humans, dimethylbenzimidazole is involved in the riboflavin metabolism pathway. Dimethylbenzimidazole has been detected, but not quantified in, a few different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), and domestic pigs (Sus scrofa domestica). This could make dimethylbenzimidazole a potential biomarker for the consumption of these foods. Dimethylbenzimidazole is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Dimethylbenzimidazole.
Structure
Data?1582752286
Synonyms
ValueSource
DimedazolChEBI
DimedazoleChEBI
DimesolChEBI
DimezolChEBI
5,6-DimethylbenzimidazoleKegg
5,6-Dimethyl-1H-benzimidazoleHMDB
DimezolDimedazolHMDB
5,6-Dimethylbenzimidazole hydrochlorideMeSH, HMDB
Chemical FormulaC9H10N2
Average Molecular Weight146.1891
Monoisotopic Molecular Weight146.08439833
IUPAC Name5,6-dimethyl-1H-1,3-benzodiazole
Traditional Name5,6-dimethylbenzimidazole
CAS Registry Number582-60-5
SMILES
CC1=CC2=C(C=C1C)N=CN2
InChI Identifier
InChI=1S/C9H10N2/c1-6-3-8-9(4-7(6)2)11-5-10-8/h3-5H,1-2H3,(H,10,11)
InChI KeyLJUQGASMPRMWIW-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
  • Heteroaromatic compound
  • Imidazole
  • Azole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Process

Naturally occurring process

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point205.5 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP1.854Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg127.72830932474
[M+H]+MetCCS_train_pos129.9330932474
[M-H]-Not Available129.3http://allccs.zhulab.cn/database/detail?ID=AllCCS00000358
[M+H]+Not Available130.3http://allccs.zhulab.cn/database/detail?ID=AllCCS00000358
Predicted Molecular Properties
PropertyValueSource
Water Solubility2.08 g/LALOGPS
logP1.88ALOGPS
logP2.29ChemAxon
logS-1.8ALOGPS
pKa (Strongest Acidic)12.73ChemAxon
pKa (Strongest Basic)6.43ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity45.05 m³·mol⁻¹ChemAxon
Polarizability16.47 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
DarkChem[M+H]+130.91431661259
DarkChem[M-H]-131.05931661259
DeepCCS[M+H]+132.58730932474
DeepCCS[M-H]-129.26830932474
DeepCCS[M-2H]-166.33430932474
DeepCCS[M+Na]+141.7130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DimethylbenzimidazoleCC1=CC2=C(C=C1C)N=CN22378.0Standard polar33892256
DimethylbenzimidazoleCC1=CC2=C(C=C1C)N=CN21588.0Standard non polar33892256
DimethylbenzimidazoleCC1=CC2=C(C=C1C)N=CN21761.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Dimethylbenzimidazole,1TMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C)C=N21760.3Semi standard non polar33892256
Dimethylbenzimidazole,1TMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C)C=N21689.1Standard non polar33892256
Dimethylbenzimidazole,1TMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C)C=N21881.2Standard polar33892256
Dimethylbenzimidazole,1TBDMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C(C)(C)C)C=N21999.0Semi standard non polar33892256
Dimethylbenzimidazole,1TBDMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C(C)(C)C)C=N21873.3Standard non polar33892256
Dimethylbenzimidazole,1TBDMS,isomer #1CC1=CC2=C(C=C1C)N([Si](C)(C)C(C)(C)C)C=N22026.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized)splash10-000t-2900000000-cf01975179c82b56a7472014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-MS (1 TMS)splash10-0gb9-5790000000-e422b94d0cbe1bd0345e2014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized)splash10-000t-2900000000-cf01975179c82b56a7472017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized)splash10-0gb9-5790000000-e422b94d0cbe1bd0345e2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-EI-TOF (Non-derivatized)splash10-000t-1900000000-1cc9a65e6235151e48202017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dimethylbenzimidazole GC-EI-TOF (Non-derivatized)splash10-0gb9-2590000000-7f1dc8fd34bdb99d58f62017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-0900000000-94a00940d804552f77d02017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dimethylbenzimidazole GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QQ , positive-QTOFsplash10-0002-0900000000-d879a610883483e633262017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QQ , positive-QTOFsplash10-0002-1900000000-7810390c926bc0a2238a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QQ , positive-QTOFsplash10-000t-3900000000-0e438f149c15e3ba22382017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QQ , positive-QTOFsplash10-000t-1900000000-286b3359932c2c63dc232017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QQ , positive-QTOFsplash10-001i-4900000000-4e9fbfe2a1943cc865e52017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QFT , negative-QTOFsplash10-0002-0900000000-4a48df4993767b5c4eff2020-07-21HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole LC-ESI-QTOF 35V, negative-QTOFsplash10-0002-0900000000-93fb22bfd73cbaaecda92020-07-21HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Positive-QTOFsplash10-0002-0900000000-5f138fc55912e09c04f82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 35V, Positive-QTOFsplash10-000t-0900000000-0ac7250afc1fd38defe32021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 20V, Positive-QTOFsplash10-0002-0900000000-941f6c90a92fad755dd02021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 40V, Positive-QTOFsplash10-001i-4900000000-9778293bbdebe312995b2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 35V, Negative-QTOFsplash10-0002-0900000000-0581e550bdf15c825ed12021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 40V, Positive-QTOFsplash10-001i-4900000000-f22be5bed413f1b519e82021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Positive-QTOFsplash10-0002-0900000000-677d27a4db0421a0c22d2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 20V, Positive-QTOFsplash10-0002-0900000000-3c2aee6880c85391a7392021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Negative-QTOFsplash10-0002-0900000000-86d65abcc3c20eeaa9b72021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 20V, Negative-QTOFsplash10-0002-0900000000-25408408c64689b319ee2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dimethylbenzimidazole 40V, Negative-QTOFsplash10-0006-1900000000-4cefb2993f948a46e8e82021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Positive-QTOFsplash10-0002-0900000000-92df1f58e19215585f6a2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 20V, Positive-QTOFsplash10-0002-0900000000-a09abdb85c0cd07661652015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 40V, Positive-QTOFsplash10-000t-2900000000-7ad608a4dad05614e9952015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Negative-QTOFsplash10-0002-0900000000-2f5826366923dad353412015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 20V, Negative-QTOFsplash10-0002-0900000000-685b19fc37ae77b7006b2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 40V, Negative-QTOFsplash10-0005-3900000000-1e116130bd866fe7fc712015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dimethylbenzimidazole 10V, Positive-QTOFsplash10-0002-0900000000-8ffc0ea3ec7f7e0434b82021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Prostate Tissue
Tissue Locations
  • Prostate
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Prostate TissueDetected and Quantified0.5 (0.0-1.0) umol/g tissueAdult (>18 years old)Both
Prostate cancer
details
Associated Disorders and Diseases
Disease References
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDDB02591
Phenol Explorer Compound IDNot Available
FooDB IDFDB023216
KNApSAcK IDNot Available
Chemspider ID655
KEGG Compound IDC03114
BioCyc IDDIMETHYLBENZIMIDAZOLE
BiGG IDNot Available
Wikipedia LinkDimethylbenzimidazole
METLIN IDNot Available
PubChem Compound675
PDB IDNot Available
ChEBI ID15890
Food Biomarker OntologyNot Available
VMH IDDMBZID
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]