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Showing metabocard for Isoindoline (HMDB0253648)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:26:58 UTC
Update Date2021-09-26 23:07:01 UTC
HMDB IDHMDB0253648
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsoindoline
DescriptionIsoindoline 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 a significant number of articles have been published on Isoindoline. This compound has been identified in human blood as reported by (PMID: 31557052 ). Isoindoline is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Isoindoline 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 HMDB0253648 (Isoindoline)


  Mrv1652309112114272D          

  9 10  0  0  0  0            999 V2000
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
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3D MOL for HMDB0253648 (Isoindoline)

HMDB0253648
     RDKit          3D
Isoindoline
 18 19  0  0  0  0  0  0  0  0999 V2000
    2.1486    1.0087    0.2152 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3002   -0.3309   -0.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2252   -1.1699   -0.3054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0623   -0.6814   -0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2507    0.6502    0.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8538    1.4827    0.2829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7116    0.8608    0.0556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2209   -0.4247    0.4772 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4267   -1.3025   -0.4074 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9831    1.6774    0.3919 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3150   -0.7020   -0.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3603   -2.2292   -0.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6914    2.5206    0.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0443    1.0181   -1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    1.6936    0.7031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8318   -0.6056    1.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8220   -1.1456   -1.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -2.3202   -0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  6  1  1  0
  9  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
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3D SDF for HMDB0253648 (Isoindoline)


  Mrv1652309112114272D          

  9 10  0  0  0  0            999 V2000
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253648

> <DATABASE_NAME>
hmdb

> <SMILES>
C1NCC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C8H9N/c1-2-4-8-6-9-5-7(8)3-1/h1-4,9H,5-6H2

> <INCHI_KEY>
GWVMLCQWXVFZCN-UHFFFAOYSA-N

> <FORMULA>
C8H9N

> <MOLECULAR_WEIGHT>
119.167

> <EXACT_MASS>
119.073499294

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
13.437085934868207

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydro-1H-isoindole

> <ALOGPS_LOGP>
0.78

> <JCHEM_LOGP>
1.282821947

> <ALOGPS_LOGS>
-0.88

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
8.878367862192889

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
37.8606

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.58e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isoindoline

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0253648 (Isoindoline)

HMDB0253648
     RDKit          3D
Isoindoline
 18 19  0  0  0  0  0  0  0  0999 V2000
    2.1486    1.0087    0.2152 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3002   -0.3309   -0.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2252   -1.1699   -0.3054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0623   -0.6814   -0.2341 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2507    0.6502    0.0609 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8538    1.4827    0.2829 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7116    0.8608    0.0556 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2209   -0.4247    0.4772 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4267   -1.3025   -0.4074 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9831    1.6774    0.3919 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3150   -0.7020   -0.1362 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3603   -2.2292   -0.5408 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6914    2.5206    0.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0443    1.0181   -1.0051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    1.6936    0.7031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8318   -0.6056    1.4505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8220   -1.1456   -1.4092 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4699   -2.3202   -0.0284 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  6  1  1  0
  9  4  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  6 13  1  0
  7 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
  9 18  1  0
M  END
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PDB for HMDB0253648 (Isoindoline)

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       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.220  -1.303   0.000  0.00  0.00           N+0
CONECT    1    2    9                                                       
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    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 HMDB0253648 (Isoindoline)

COMPND    HMDB0253648
HETATM    1  C1  UNL     1       2.149   1.009   0.215  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.300  -0.331  -0.083  1.00  0.00           C  
HETATM    3  C3  UNL     1       1.225  -1.170  -0.305  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.062  -0.681  -0.234  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.251   0.650   0.061  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.854   1.483   0.283  1.00  0.00           C  
HETATM    7  C7  UNL     1      -1.712   0.861   0.056  1.00  0.00           C  
HETATM    8  N1  UNL     1      -2.221  -0.425   0.477  1.00  0.00           N  
HETATM    9  C8  UNL     1      -1.427  -1.303  -0.407  1.00  0.00           C  
HETATM   10  H1  UNL     1       2.983   1.677   0.392  1.00  0.00           H  
HETATM   11  H2  UNL     1       3.315  -0.702  -0.136  1.00  0.00           H  
HETATM   12  H3  UNL     1       1.360  -2.229  -0.541  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.691   2.521   0.513  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.044   1.018  -1.005  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.037   1.694   0.703  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.832  -0.606   1.450  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.822  -1.146  -1.409  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.470  -2.320  -0.028  1.00  0.00           H  
CONECT    1    2    2    6   10
CONECT    2    3   11
CONECT    3    4    4   12
CONECT    4    5    9
CONECT    5    6    6    7
CONECT    6   13
CONECT    7    8   14   15
CONECT    8    9   16
CONECT    9   17   18
END
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SMILES for HMDB0253648 (Isoindoline)

C1NCC2=CC=CC=C12
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INCHI for HMDB0253648 (Isoindoline)

InChI=1S/C8H9N/c1-2-4-8-6-9-5-7(8)3-1/h1-4,9H,5-6H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H9N
Average Molecular Weight119.167
Monoisotopic Molecular Weight119.073499294
IUPAC Name2,3-dihydro-1H-isoindole
Traditional Nameisoindoline
CAS Registry NumberNot Available
SMILES
C1NCC2=CC=CC=C12
InChI Identifier
InChI=1S/C8H9N/c1-2-4-8-6-9-5-7(8)3-1/h1-4,9H,5-6H2
InChI KeyGWVMLCQWXVFZCN-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
  • Isoindoline
  • Aralkylamine
  • Benzenoid
  • Azacycle
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Amine
  • 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
logP0.78ALOGPS
logP1.28ChemAxon
logS-0.88ALOGPS
pKa (Strongest Basic)8.88ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.03 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity37.86 m³·mol⁻¹ChemAxon
Polarizability13.44 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-2H]-158.11430932474
DeepCCS[M+Na]+132.9430932474
AllCCS[M+H]+122.932859911
AllCCS[M+H-H2O]+117.932859911
AllCCS[M+NH4]+127.632859911
AllCCS[M+Na]+129.032859911
AllCCS[M-H]-122.832859911
AllCCS[M+Na-2H]-124.432859911
AllCCS[M+HCOO]-126.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IsoindolineC1NCC2=CC=CC=C122010.1Standard polar33892256
IsoindolineC1NCC2=CC=CC=C121126.3Standard non polar33892256
IsoindolineC1NCC2=CC=CC=C121151.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Isoindoline,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C11377.7Semi standard non polar33892256
Isoindoline,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C11263.1Standard non polar33892256
Isoindoline,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C11569.9Standard polar33892256
Isoindoline,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C11605.7Semi standard non polar33892256
Isoindoline,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C11507.3Standard non polar33892256
Isoindoline,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C11784.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Isoindoline GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-5900000000-f8b1a3aa64a3f089ab5e2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isoindoline 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 - Isoindoline 10V, Positive-QTOFsplash10-00di-1900000000-255a686469c694d9ad7e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindoline 20V, Positive-QTOFsplash10-0fdo-6900000000-72d91cf170abfec89e942021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindoline 40V, Positive-QTOFsplash10-0f6x-9200000000-676a110a7774be863c6a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindoline 10V, Negative-QTOFsplash10-014i-0900000000-027d0d4be6036ac052f52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindoline 20V, Negative-QTOFsplash10-014i-2900000000-644a57f29c406c463c5b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindoline 40V, Negative-QTOFsplash10-014l-7900000000-fd31dcdfdb971a239def2021-10-12Wishart 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 ID373951
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIsoindoline
METLIN IDNot Available
PubChem Compound422478
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 ]