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Showing metabocard for Isoindolin-1-one (HMDB0253647)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:26:54 UTC
Update Date2021-09-26 23:07:01 UTC
HMDB IDHMDB0253647
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsoindolin-1-one
Descriptionisoindolin-1-one, also known as 1-oxo-isoindoline or phthalimidine, belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone. Based on a literature review very few articles have been published on isoindolin-1-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Isoindolin-1-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Isoindolin-1-one 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 HMDB0253647 (Isoindolin-1-one)


  Mrv1652309112114272D          

 10 11  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
    0.8838   -2.1500    0.0000 O   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  2  0  0  0  0
  8 10  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0253647 (Isoindolin-1-one)

HMDB0253647
     RDKit          3D
Isoindolin-1-one
 17 18  0  0  0  0  0  0  0  0999 V2000
   -1.6483    2.6041   -0.2129 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4193    1.3758   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    0.3243   -0.1443 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6714   -0.9261   -0.0489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2385   -0.5923    0.0131 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8726   -1.4455    0.1131 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0948   -0.8169    0.1499 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2801    0.5260    0.0970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1808    1.3490   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0975    0.7734   -0.0432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4135    0.4577   -0.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9364   -1.4805    0.8983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710   -1.5893   -0.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7559   -2.5227    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9634   -1.4625    0.2271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2696    0.9994    0.1284 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2317    2.4262   -0.0487 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0253647 (Isoindolin-1-one)


  Mrv1652309112114272D          

 10 11  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
    0.8838   -2.1500    0.0000 O   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  2  0  0  0  0
  8 10  1  0  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253647

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1NCC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C8H7NO/c10-8-7-4-2-1-3-6(7)5-9-8/h1-4H,5H2,(H,9,10)

> <INCHI_KEY>
PXZQEOJJUGGUIB-UHFFFAOYSA-N

> <FORMULA>
C8H7NO

> <MOLECULAR_WEIGHT>
133.15

> <EXACT_MASS>
133.052763849

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.590318951065841

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydro-1H-isoindol-1-one

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
0.7987894773333332

> <ALOGPS_LOGS>
-1.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.04782296723352

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.041406725598574

> <JCHEM_PKA_STRONGEST_BASIC>
-1.207925137066074

> <JCHEM_POLAR_SURFACE_AREA>
29.1

> <JCHEM_REFRACTIVITY>
38.5877

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.37e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydro-1H-isoindol-1-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0253647 (Isoindolin-1-one)

HMDB0253647
     RDKit          3D
Isoindolin-1-one
 17 18  0  0  0  0  0  0  0  0999 V2000
   -1.6483    2.6041   -0.2129 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4193    1.3758   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3531    0.3243   -0.1443 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6714   -0.9261   -0.0489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2385   -0.5923    0.0131 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8726   -1.4455    0.1131 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0948   -0.8169    0.1499 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2801    0.5260    0.0970 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1808    1.3490   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0975    0.7734   -0.0432 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4135    0.4577   -0.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9364   -1.4805    0.8983 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8710   -1.5893   -0.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7559   -2.5227    0.1573 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9634   -1.4625    0.2271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2696    0.9994    0.1284 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2317    2.4262   -0.0487 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
 10  5  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0253647 (Isoindolin-1-one)

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  O   UNK     0       1.650  -4.013   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0       1.220  -1.303   0.000  0.00  0.00           N+0
CONECT    1    2   10                                                       
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   10                                                  
CONECT    9    8                                                            
CONECT   10    8    1                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0253647 (Isoindolin-1-one)

COMPND    HMDB0253647
HETATM    1  O1  UNL     1      -1.648   2.604  -0.213  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.419   1.376  -0.143  1.00  0.00           C  
HETATM    3  N1  UNL     1      -2.353   0.324  -0.144  1.00  0.00           N  
HETATM    4  C2  UNL     1      -1.671  -0.926  -0.049  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.238  -0.592   0.013  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.873  -1.445   0.113  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.095  -0.817   0.150  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.280   0.526   0.097  1.00  0.00           C  
HETATM    9  C7  UNL     1       1.181   1.349  -0.001  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.098   0.773  -0.043  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.413   0.458  -0.208  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.936  -1.481   0.898  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.871  -1.589  -0.934  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.756  -2.523   0.157  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.963  -1.463   0.227  1.00  0.00           H  
HETATM   16  H6  UNL     1       3.270   0.999   0.128  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.232   2.426  -0.049  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4   11
CONECT    4    5   12   13
CONECT    5    6    6   10
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9   16
CONECT    9   10   10   17
END
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SMILES for HMDB0253647 (Isoindolin-1-one)

O=C1NCC2=CC=CC=C12
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INCHI for HMDB0253647 (Isoindolin-1-one)

InChI=1S/C8H7NO/c10-8-7-4-2-1-3-6(7)5-9-8/h1-4H,5H2,(H,9,10)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1-oxo-IsoindolineChEBI
2,3-Dihydro-1H-isoindol-1-oneChEBI
2,3-Dihydro-3-oxo-1H-isoindoleChEBI
Dihydro-isoindol-1-oneChEBI
IsoindolinoneMeSH
PhthalimidineMeSH
Chemical FormulaC8H7NO
Average Molecular Weight133.15
Monoisotopic Molecular Weight133.052763849
IUPAC Name2,3-dihydro-1H-isoindol-1-one
Traditional Name2,3-dihydro-1H-isoindol-1-one
CAS Registry NumberNot Available
SMILES
O=C1NCC2=CC=CC=C12
InChI Identifier
InChI=1S/C8H7NO/c10-8-7-4-2-1-3-6(7)5-9-8/h1-4H,5H2,(H,9,10)
InChI KeyPXZQEOJJUGGUIB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isoindolones. These are aromatic polycyclic compounds that an isoindole bearing a ketone.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIsoindoles and derivatives
Sub ClassIsoindolines
Direct ParentIsoindolones
Alternative Parents
Substituents
  • Isoindolone
  • Isoindole
  • Benzenoid
  • Carboxamide group
  • Lactam
  • Secondary carboxylic acid amide
  • Carboxylic acid derivative
  • Azacycle
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
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
logP0.64ALOGPS
logP0.8ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)14.04ChemAxon
pKa (Strongest Basic)-1.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area29.1 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity38.59 m³·mol⁻¹ChemAxon
Polarizability13.59 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]-159.41430932474
DeepCCS[M+Na]+134.43230932474
AllCCS[M+H]+130.832859911
AllCCS[M+H-H2O]+126.232859911
AllCCS[M+NH4]+135.132859911
AllCCS[M+Na]+136.332859911
AllCCS[M-H]-124.432859911
AllCCS[M+Na-2H]-125.832859911
AllCCS[M+HCOO]-127.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Isoindolin-1-oneO=C1NCC2=CC=CC=C122599.7Standard polar33892256
Isoindolin-1-oneO=C1NCC2=CC=CC=C121425.4Standard non polar33892256
Isoindolin-1-oneO=C1NCC2=CC=CC=C121512.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Isoindolin-1-one,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C1=O1533.1Semi standard non polar33892256
Isoindolin-1-one,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C1=O1486.0Standard non polar33892256
Isoindolin-1-one,1TMS,isomer #1C[Si](C)(C)N1CC2=CC=CC=C2C1=O1791.6Standard polar33892256
Isoindolin-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C1=O1762.2Semi standard non polar33892256
Isoindolin-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C1=O1728.8Standard non polar33892256
Isoindolin-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)N1CC2=CC=CC=C2C1=O1997.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Isoindolin-1-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-053r-2900000000-48d48385456fa7ff14912021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isoindolin-1-one 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 - Isoindolin-1-one 10V, Positive-QTOFsplash10-001i-0900000000-ac524f6f858437766e2f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindolin-1-one 20V, Positive-QTOFsplash10-001i-3900000000-349cf828e71f48701c012021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindolin-1-one 40V, Positive-QTOFsplash10-004i-9400000000-101e1162697045bab0d62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindolin-1-one 10V, Negative-QTOFsplash10-001i-0900000000-a956a3a0009c6965897a2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindolin-1-one 20V, Negative-QTOFsplash10-001i-2900000000-cc2af5e89fab3ba83fc82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoindolin-1-one 40V, Negative-QTOFsplash10-0ue9-6900000000-721b1ccba220693e79232021-10-12Wishart 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 IDC00029429
Chemspider ID9784
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10199
PDB IDNot Available
ChEBI ID74235
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 ]