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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:49 UTC
Update Date2022-03-07 02:51:39 UTC
HMDB IDHMDB0014550
Secondary Accession Numbers
  • HMDB14550
Metabolite Identification
Common NameGentian Violet
DescriptionGentian Violet is only found in individuals that have used or taken this drug. It is a dye that is a mixture of violet rosanilinis with antibacterial, antifungal, and anthelmintic properties. [PubChem]In aqueous solutions Gentian violet (GV) dissociates into positive (GV+)and negative ions (Cl-) that penetrate through the wall and membrane of both gram-positive and gram-negative bacterial cells. The GV+ interacts with negatively charged components of bacterial cells including the lipopolysaccharide (on the cell wall), the peptidoglycan and DNA. A similar cell penetration and DNA binding process is thought to take place for fungal cells as well. Because Gentian violet is a mutagen and mitotic poison, cell growth is consequently inhibited. A photodynamic action of gentian violet, apparently mediated by a free-radical mechanism, has recently been described in bacteria and in the protozoan T. cruzi. Evidence also suggests that gentian violet dissipates the bacterial (and mitochondrial) membrane potential by inducing permeability. This is followed by respiratory inhibition. This anti-mitochondrial activity might explain gentian violet's efficacy towards both bacteria and yeast with relatively mild effects on mammalian cells.
Structure
Data?1582753192
Synonyms
ValueSource
Crystal violet carbocationChEBI
Crystal violet ion(1)ChEBI
Crystal violet(1+)ChEBI
Gentian violet carbocationChEBI
Gentian violet cationChEBI
Gentian violet(1+)ChEBI
Crystal violetHMDB
Chemical FormulaC25H30N3
Average Molecular Weight372.5258
Monoisotopic Molecular Weight372.243972975
IUPAC Name4-{bis[4-(dimethylamino)phenyl]methylidene}-N,N-dimethylcyclohexa-2,5-dien-1-iminium
Traditional Namegentian violet
CAS Registry Number14426-25-6
SMILES
CN(C)C1=CC=C(C=C1)C(C1=CC=C(C=C1)N(C)C)=C1C=CC(C=C1)=[N+](C)C
InChI Identifier
InChI=1S/C25H30N3/c1-26(2)22-13-7-19(8-14-22)25(20-9-15-23(16-10-20)27(3)4)21-11-17-24(18-12-21)28(5)6/h7-18H,1-6H3/q+1
InChI KeyLGLFFNDHMLKUMI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diphenylmethanes. Diphenylmethanes are compounds containing a diphenylmethane moiety, which consists of a methane wherein two hydrogen atoms are replaced by two phenyl groups.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassDiphenylmethanes
Direct ParentDiphenylmethanes
Alternative Parents
Substituents
  • Diphenylmethane
  • Aniline or substituted anilines
  • Dialkylarylamine
  • Tertiary aliphatic/aromatic amine
  • Secondary ketimine
  • Azomethine
  • Tertiary amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • Organic cation
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point215 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.0019 g/LNot Available
LogP3.18Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0019 g/LALOGPS
logP0.87ALOGPS
logP1.4ChemAxon
logS-5.3ALOGPS
pKa (Strongest Basic)4.83ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area9.49 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity146 m³·mol⁻¹ChemAxon
Polarizability45.6 ųChemAxon
Number of Rings3ChemAxon
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]+205.65530932474
DeepCCS[M-H]-203.25930932474
DeepCCS[M-2H]-236.14430932474
DeepCCS[M+Na]+211.68430932474
AllCCS[M+H]+194.432859911
AllCCS[M+H-H2O]+191.632859911
AllCCS[M+NH4]+197.032859911
AllCCS[M+Na]+197.832859911
AllCCS[M-H]-199.932859911
AllCCS[M+Na-2H]-200.532859911
AllCCS[M+HCOO]-201.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Gentian VioletCN(C)C1=CC=C(C=C1)C(C1=CC=C(C=C1)N(C)C)=C1C=CC(C=C1)=[N+](C)C4321.0Standard polar33892256
Gentian VioletCN(C)C1=CC=C(C=C1)C(C1=CC=C(C=C1)N(C)C)=C1C=CC(C=C1)=[N+](C)C3205.4Standard non polar33892256
Gentian VioletCN(C)C1=CC=C(C=C1)C(C1=CC=C(C=C1)N(C)C)=C1C=CC(C=C1)=[N+](C)C3798.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Gentian Violet GC-MS (Non-derivatized) - 70eV, Positivesplash10-0pi0-3049000000-80f825970014ad3163432017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gentian Violet 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 - Gentian Violet 10V, Positive-QTOFsplash10-00di-0009000000-a180c3b409add42945482016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 20V, Positive-QTOFsplash10-00di-1009000000-280bb4ba1bf4de1f499c2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 40V, Positive-QTOFsplash10-00di-9134000000-e868f5dd8c887ae091882016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 10V, Negative-QTOFsplash10-00di-0009000000-04443be1085d68e129812016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 20V, Negative-QTOFsplash10-00di-0009000000-6c18d897813c5e051baa2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 40V, Negative-QTOFsplash10-00xr-9007000000-e9e03d7198bf6e7ffaf72016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 10V, Positive-QTOFsplash10-00di-0009000000-d19ae55e6f44c6c20e812021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 20V, Positive-QTOFsplash10-00di-0009000000-fa424c62ab49e37237972021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gentian Violet 40V, Positive-QTOFsplash10-100c-0049000000-e89b52ae60e84c397fa52021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00406 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00406 details
Abnormal Concentrations
Not Available
Predicted Concentrations
BiospecimenValueOriginal ageOriginal sexOriginal conditionComments
Blood0.000 uMAdult (>18 years old)BothNormalPredicted based on drug qualities
Blood0.000 umol/mmol creatinineAdult (>18 years old)BothNormalPredicted based on drug qualities
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00406
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID3349
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCrystal violet
METLIN IDNot Available
PubChem Compound3468
PDB IDCVI
ChEBI ID77181
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 ReferencesNot Available

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Translocates a broad array of organic cations with various structures and molecular weights including the model compounds 1-methyl-4-phenylpyridinium (MPP), tetraethylammonium (TEA), N-1-methylnicotinamide (NMN), 4-(4-(dimethylamino)styryl)- N-methylpyridinium (ASP), the endogenous compounds choline, guanidine, histamine, epinephrine, adrenaline, noradrenaline and dopamine, and the drugs quinine, and metformin. The transport of organic cations is inhibited by a broad array of compounds like tetramethylammonium (TMA), cocaine, lidocaine, NMDA receptor antagonists, atropine, prazosin, cimetidine, TEA and NMN, guanidine, cimetidine, choline, procainamide, quinine, tetrabutylammonium, and tetrapentylammonium. Translocates organic cations in an electrogenic and pH-independent manner. Translocates organic cations across the plasma membrane in both directions. Transports the polyamines spermine and spermidine. Transports pramipexole across the basolateral membrane of the proximal tubular epithelial cells. The choline transport is activated by MMTS. Regulated by various intracellular signaling pathways including inhibition by protein kinase A activation, and endogenously activation by the calmodulin complex, the calmodulin- dependent kinase II and LCK tyrosine kinase
Gene Name:
SLC22A1
Uniprot ID:
O15245
Molecular weight:
61187.4
References
  1. Bednarczyk D, Ekins S, Wikel JH, Wright SH: Influence of molecular structure on substrate binding to the human organic cation transporter, hOCT1. Mol Pharmacol. 2003 Mar;63(3):489-98. [PubMed:12606755 ]