Hmdb loader
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 00:02:33 UTC
Update Date2021-09-26 22:56:28 UTC
HMDB IDHMDB0247024
Secondary Accession NumbersNone
Metabolite Identification
Common Name5H-Pyrido[4,3-b]indole
Description5H-Pyrido[4,3-b]indole, also known as gamma-carboline, belongs to the class of organic compounds known as gamma carbolines. These are polycyclic aromatic compounds containing a gamma-carbazole(5H-pyrido[4,3-b]indole) moiety, with a structure characterized by the presence of pyridine fused to the pyrrole ring of an indole. Based on a literature review very few articles have been published on 5H-Pyrido[4,3-b]indole. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5h-pyrido[4,3-b]indole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5H-Pyrido[4,3-b]indole 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
Thumb
Synonyms
ValueSource
gamma-CarbolineMeSH
gamma-Carboline hydrochlorideMeSH
gamma-Carboline monohydrochlorideMeSH
Chemical FormulaC11H8N2
Average Molecular Weight168.199
Monoisotopic Molecular Weight168.068748266
IUPAC Name5H-pyrido[4,3-b]indole
Traditional Name5H-pyrido[4,3-b]indole
CAS Registry NumberNot Available
SMILES
N1C2=CC=CC=C2C2=C1C=CN=C2
InChI Identifier
InChI=1S/C11H8N2/c1-2-4-10-8(3-1)9-7-12-6-5-11(9)13-10/h1-7,13H
InChI KeyRDMFHRSPDKWERA-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma carbolines. These are polycyclic aromatic compounds containing a gamma-carbazole(5H-pyrido[4,3-b]indole) moiety, with a structure characterized by the presence of pyridine fused to the pyrrole ring of an indole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassPyridoindoles
Direct ParentGamma carbolines
Alternative Parents
Substituents
  • Gamma-carboline
  • Pyrrolopyridine
  • Indole
  • Benzenoid
  • Pyridine
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
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
logP2.54ALOGPS
logP1.87ChemAxon
logS-2.7ALOGPS
pKa (Strongest Acidic)13.19ChemAxon
pKa (Strongest Basic)8.13ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area28.68 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity51.32 m³·mol⁻¹ChemAxon
Polarizability18.09 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+130.76130932474
DeepCCS[M-H]-127.96830932474
DeepCCS[M-2H]-164.42630932474
DeepCCS[M+Na]+139.82330932474
AllCCS[M+H]+134.732859911
AllCCS[M+H-H2O]+130.032859911
AllCCS[M+NH4]+139.132859911
AllCCS[M+Na]+140.432859911
AllCCS[M-H]-136.432859911
AllCCS[M+Na-2H]-136.332859911
AllCCS[M+HCOO]-136.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5H-Pyrido[4,3-b]indoleN1C2=CC=CC=C2C2=C1C=CN=C22859.6Standard polar33892256
5H-Pyrido[4,3-b]indoleN1C2=CC=CC=C2C2=C1C=CN=C21829.9Standard non polar33892256
5H-Pyrido[4,3-b]indoleN1C2=CC=CC=C2C2=C1C=CN=C22071.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5H-Pyrido[4,3-b]indole,1TMS,isomer #1C[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C212066.6Semi standard non polar33892256
5H-Pyrido[4,3-b]indole,1TMS,isomer #1C[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C211884.0Standard non polar33892256
5H-Pyrido[4,3-b]indole,1TMS,isomer #1C[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C212321.6Standard polar33892256
5H-Pyrido[4,3-b]indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C212334.1Semi standard non polar33892256
5H-Pyrido[4,3-b]indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C212074.8Standard non polar33892256
5H-Pyrido[4,3-b]indole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C2=CC=CC=C2C2=CN=CC=C212406.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5H-Pyrido[4,3-b]indole GC-MS (Non-derivatized) - 70eV, Positivesplash10-0gbc-0900000000-cd532501e5722766fa932021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5H-Pyrido[4,3-b]indole 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 - 5H-Pyrido[4,3-b]indole 50V, Positive-QTOFsplash10-014l-0900000000-790b9d51615ce67894422021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 40V, Positive-QTOFsplash10-014i-0900000000-f5981a2a8ad165d5b1442021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 40V, Positive-QTOFsplash10-014i-0900000000-a4701e267486987276902021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 30V, Positive-QTOFsplash10-014i-0900000000-319c5b06a3fb605d32f42021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 20V, Positive-QTOFsplash10-014i-0900000000-10d96f6be36f255ddc142021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 61V, Positive-QTOFsplash10-014i-0900000000-10004847a6fcf5b592522021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 10V, Positive-QTOFsplash10-014i-0900000000-86c1b05392b6d7ed61a22021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 10V, Positive-QTOFsplash10-014i-0900000000-d82f3470533b3efe7f962021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 20V, Positive-QTOFsplash10-014i-0900000000-d82f3470533b3efe7f962021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 40V, Positive-QTOFsplash10-014i-0900000000-82c59e70547a3a3256a32021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 10V, Negative-QTOFsplash10-014i-0900000000-1ba6c7cf3004ee08cdb72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 20V, Negative-QTOFsplash10-014i-0900000000-1ba6c7cf3004ee08cdb72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5H-Pyrido[4,3-b]indole 40V, Negative-QTOFsplash10-014i-0900000000-1ba6c7cf3004ee08cdb72021-10-12Wishart 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 ID115684
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound130802
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 ]