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Showing metabocard for Isoindole (HMDB0245764)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:49:03 UTC
Update Date2021-09-26 22:54:25 UTC
HMDB IDHMDB0245764
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsoindole
Description2H-isoindole belongs to the class of organic compounds known as isoindoles. These are heteropolycyclic compounds with a structure containing isoindole, a benzo-fused pyrrole. Based on a literature review very few articles have been published on 2H-isoindole. This compound has been identified in human blood as reported by (PMID: 31557052 ). Isoindole is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Isoindole 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 HMDB0245764 (Isoindole)


  Mrv1652309112100492D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   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  1  0  0  0  0
  6  7  2  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
M  END
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3D MOL for HMDB0245764 (Isoindole)

HMDB0245764
     RDKit          3D
Isoindole
 16 17  0  0  0  0  0  0  0  0999 V2000
   -1.9923    0.9849    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1354   -0.3830    0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0498   -1.2254   -0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2383   -0.7286   -0.0565 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4867   -1.3228   -0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3801   -0.3066   -0.0791 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7524    0.8728    0.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3867    0.6493    0.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7064    1.5000    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8711    1.6081    0.1817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1234   -0.8687    0.0153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1509   -2.2963   -0.1320 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6952   -2.3976   -0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4183   -0.4886   -0.1170 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2155    1.8489    0.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5440    2.5536    0.1911 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  1  2  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
M  END
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3D SDF for HMDB0245764 (Isoindole)


  Mrv1652309112100492D          

  9 10  0  0  0  0            999 V2000
    2.0701    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701    1.9354    0.0000 C   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  1  0  0  0  0
  6  7  2  0  0  0  0
  3  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245764

> <DATABASE_NAME>
hmdb

> <SMILES>
N1C=C2C=CC=CC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C8H7N/c1-2-4-8-6-9-5-7(8)3-1/h1-6,9H

> <INCHI_KEY>
VHMICKWLTGFITH-UHFFFAOYSA-N

> <FORMULA>
C8H7N

> <MOLECULAR_WEIGHT>
117.151

> <EXACT_MASS>
117.057849229

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.775273588346607

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2H-isoindole

> <ALOGPS_LOGP>
2.26

> <JCHEM_LOGP>
2.0426066853333333

> <ALOGPS_LOGS>
-1.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.826229675314256

> <JCHEM_POLAR_SURFACE_AREA>
15.79

> <JCHEM_REFRACTIVITY>
37.26700000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.31e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2H-isoindole

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245764 (Isoindole)

HMDB0245764
     RDKit          3D
Isoindole
 16 17  0  0  0  0  0  0  0  0999 V2000
   -1.9923    0.9849    0.1170 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1354   -0.3830    0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0498   -1.2254   -0.0598 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2383   -0.7286   -0.0565 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4867   -1.3228   -0.1282 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3801   -0.3066   -0.0791 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7524    0.8728    0.0182 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3867    0.6493    0.0358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7064    1.5000    0.1216 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8711    1.6081    0.1817 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1234   -0.8687    0.0153 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1509   -2.2963   -0.1320 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6952   -2.3976   -0.2081 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4183   -0.4886   -0.1170 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2155    1.8489    0.0750 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5440    2.5536    0.1911 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  2  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9  1  2  0
  8  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
M  END
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PDB for HMDB0245764 (Isoindole)

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       3.864   2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.530   1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.197   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.268   1.597   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      -1.173   2.843   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      -0.268   4.089   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8    1                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0245764 (Isoindole)

COMPND    HMDB0245764
HETATM    1  C1  UNL     1      -1.992   0.985   0.117  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.135  -0.383   0.025  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.050  -1.225  -0.060  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.238  -0.729  -0.057  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.487  -1.323  -0.128  1.00  0.00           C  
HETATM    6  N1  UNL     1       2.380  -0.307  -0.079  1.00  0.00           N  
HETATM    7  C6  UNL     1       1.752   0.873   0.018  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.387   0.649   0.036  1.00  0.00           C  
HETATM    9  C8  UNL     1      -0.706   1.500   0.122  1.00  0.00           C  
HETATM   10  H1  UNL     1      -2.871   1.608   0.182  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.123  -0.869   0.015  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.151  -2.296  -0.132  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.695  -2.398  -0.208  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.418  -0.489  -0.117  1.00  0.00           H  
HETATM   15  H6  UNL     1       2.216   1.849   0.075  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.544   2.554   0.191  1.00  0.00           H  
CONECT    1    2    9    9   10
CONECT    2    3    3   11
CONECT    3    4   12
CONECT    4    5    5    8
CONECT    5    6   13
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9
CONECT    9   16
END
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SMILES for HMDB0245764 (Isoindole)

N1C=C2C=CC=CC2=C1
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INCHI for HMDB0245764 (Isoindole)

InChI=1S/C8H7N/c1-2-4-8-6-9-5-7(8)3-1/h1-6,9H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
IsoindolesMeSH
Chemical FormulaC8H7N
Average Molecular Weight117.151
Monoisotopic Molecular Weight117.057849229
IUPAC Name2H-isoindole
Traditional Name2H-isoindole
CAS Registry NumberNot Available
SMILES
N1C=C2C=CC=CC2=C1
InChI Identifier
InChI=1S/C8H7N/c1-2-4-8-6-9-5-7(8)3-1/h1-6,9H
InChI KeyVHMICKWLTGFITH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isoindoles. These are heteropolycyclic compounds with a structure containing isoindole, a benzo-fused pyrrole.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIsoindoles and derivatives
Sub ClassIsoindoles
Direct ParentIsoindoles
Alternative Parents
Substituents
  • Isoindole
  • Benzenoid
  • Heteroaromatic compound
  • Pyrrole
  • Azacycle
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Not AvailableNot 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
logP2.26ALOGPS
logP2.04ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)16.83ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area15.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.27 m³·mol⁻¹ChemAxon
Polarizability12.78 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]+123.12630932474
DeepCCS[M-H]-120.75230932474
DeepCCS[M-2H]-157.0430932474
DeepCCS[M+Na]+131.97430932474
AllCCS[M+H]+122.432859911
AllCCS[M+H-H2O]+117.332859911
AllCCS[M+NH4]+127.132859911
AllCCS[M+Na]+128.532859911
AllCCS[M-H]-119.332859911
AllCCS[M+Na-2H]-120.832859911
AllCCS[M+HCOO]-122.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IsoindoleN1C=C2C=CC=CC2=C12403.5Standard polar33892256
IsoindoleN1C=C2C=CC=CC2=C11243.8Standard non polar33892256
IsoindoleN1C=C2C=CC=CC2=C11308.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Isoindole,1TMS,isomer #1C[Si](C)(C)N1C=C2C=CC=CC2=C11470.8Semi standard non polar33892256
Isoindole,1TMS,isomer #1C[Si](C)(C)N1C=C2C=CC=CC2=C11427.6Standard non polar33892256
Isoindole,1TMS,isomer #1C[Si](C)(C)N1C=C2C=CC=CC2=C11734.2Standard polar33892256
Isoindole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=C2C=CC=CC2=C11732.9Semi standard non polar33892256
Isoindole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=C2C=CC=CC2=C11617.7Standard non polar33892256
Isoindole,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1C=C2C=CC=CC2=C11882.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Isoindole GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-4900000000-e28e28dff45d42b564d62021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isoindole 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 - Isoindole 10V, Positive-QTOFsplash10-014i-0900000000-64f3023d9e0482ad4e6f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindole 20V, Positive-QTOFsplash10-014i-0900000000-64f3023d9e0482ad4e6f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindole 40V, Positive-QTOFsplash10-00ko-9100000000-0cefafdcd77ac006eeb82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindole 10V, Negative-QTOFsplash10-014i-0900000000-89c3f30c8225ba6d5d622021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindole 20V, Negative-QTOFsplash10-014i-0900000000-89c3f30c8225ba6d5d622021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindole 40V, Negative-QTOFsplash10-014i-0900000000-89c3f30c8225ba6d5d622021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart 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 ID2282425
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIsoindole
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID33179
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 ]