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Showing metabocard for Indol-2-One (HMDB0253466)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:54:54 UTC
Update Date2022-11-23 22:13:43 UTC
HMDB IDHMDB0253466
Secondary Accession NumbersNone
Metabolite Identification
Common NameIndol-2-One
Descriptionindol-2-one belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Based on a literature review a significant number of articles have been published on indol-2-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). Indol-2-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Indol-2-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 HMDB0253466 (Indol-2-One)


  Mrv1652309112113552D          

 10 11  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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   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  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  1 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0253466 (Indol-2-One)

HMDB0253466
     RDKit          3D
indol-2-one
 15 16  0  0  0  0  0  0  0  0999 V2000
    3.8291   -0.3150   -0.0236 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5707   -0.2658   -0.0200 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7652    0.9469    0.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4890    0.5500    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110    1.2487    0.0954 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9217    0.5908    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9931   -0.7767   -0.0597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8143   -1.4868   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998   -0.8211   -0.0628 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6162   -1.3157   -0.1004 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0634    1.9745    0.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6402    2.3386    0.1788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8376    1.1885    0.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9654   -1.2975   -0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8500   -2.5594   -0.1959 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
  9  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  8 15  1  0
M  END
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3D SDF for HMDB0253466 (Indol-2-One)


  Mrv1652309112113552D          

 10 11  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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    1.5229    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435    2.1904    0.0000 N   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  2  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253466

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1C=C2C=CC=CC2=N1

> <INCHI_IDENTIFIER>
InChI=1S/C8H5NO/c10-8-5-6-3-1-2-4-7(6)9-8/h1-5H

> <INCHI_KEY>
QNLOWBMKUIXCOW-UHFFFAOYSA-N

> <FORMULA>
C8H5NO

> <MOLECULAR_WEIGHT>
131.134

> <EXACT_MASS>
131.037113785

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
12.984840035154352

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2H-indol-2-one

> <ALOGPS_LOGP>
1.20

> <JCHEM_LOGP>
0.7740543336666666

> <ALOGPS_LOGS>
-1.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
0.8763817503483432

> <JCHEM_POLAR_SURFACE_AREA>
29.43

> <JCHEM_REFRACTIVITY>
40.930099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indol-2-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0253466 (Indol-2-One)

HMDB0253466
     RDKit          3D
indol-2-one
 15 16  0  0  0  0  0  0  0  0999 V2000
    3.8291   -0.3150   -0.0236 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5707   -0.2658   -0.0200 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7652    0.9469    0.0726 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4890    0.5500    0.0421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7110    1.2487    0.0954 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9217    0.5908    0.0449 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9931   -0.7767   -0.0597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8143   -1.4868   -0.1138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3998   -0.8211   -0.0628 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6162   -1.3157   -0.1004 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0634    1.9745    0.1513 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6402    2.3386    0.1788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8376    1.1885    0.0905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9654   -1.2975   -0.0996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8500   -2.5594   -0.1959 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10  2  1  0
  9  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0253466 (Indol-2-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       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  C   UNK     0      -1.173   2.843   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -2.713   2.843   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0      -0.268   4.089   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.197   3.613   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.530   4.383   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.864   3.613   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9    1                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   22    0
END
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3D PDB for HMDB0253466 (Indol-2-One)

COMPND    HMDB0253466
HETATM    1  O1  UNL     1       3.829  -0.315  -0.024  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.571  -0.266  -0.020  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.765   0.947   0.073  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.489   0.550   0.042  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.711   1.249   0.095  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.922   0.591   0.045  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.993  -0.777  -0.060  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.814  -1.487  -0.114  1.00  0.00           C  
HETATM    9  C8  UNL     1       0.400  -0.821  -0.063  1.00  0.00           C  
HETATM   10  N1  UNL     1       1.616  -1.316  -0.100  1.00  0.00           N  
HETATM   11  H1  UNL     1       2.063   1.975   0.151  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.640   2.339   0.179  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.838   1.189   0.091  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.965  -1.297  -0.100  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.850  -2.559  -0.196  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   10
CONECT    3    4    4   11
CONECT    4    5    9
CONECT    5    6    6   12
CONECT    6    7   13
CONECT    7    8    8   14
CONECT    8    9   15
CONECT    9   10   10
END
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SMILES for HMDB0253466 (Indol-2-One)

O=C1C=C2C=CC=CC2=N1
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INCHI for HMDB0253466 (Indol-2-One)

InChI=1S/C8H5NO/c10-8-5-6-3-1-2-4-7(6)9-8/h1-5H
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC8H5NO
Average Molecular Weight131.134
Monoisotopic Molecular Weight131.037113785
IUPAC Name2H-indol-2-one
Traditional Nameindol-2-one
CAS Registry NumberNot Available
SMILES
O=C1C=C2C=CC=CC2=N1
InChI Identifier
InChI=1S/C8H5NO/c10-8-5-6-3-1-2-4-7(6)9-8/h1-5H
InChI KeyQNLOWBMKUIXCOW-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassIndoles and derivatives
Sub ClassNot Available
Direct ParentIndoles and derivatives
Alternative Parents
Substituents
  • Indole or derivatives
  • Benzenoid
  • N-acylimine
  • Azacycle
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • 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
logP1.2ALOGPS
logP0.77ChemAxon
logS-2ALOGPS
pKa (Strongest Basic)0.88ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area29.43 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity40.93 m³·mol⁻¹ChemAxon
Polarizability12.98 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]+124.46230932474
DeepCCS[M-H]-120.66730932474
DeepCCS[M-2H]-158.08930932474
DeepCCS[M+Na]+133.30130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
indol-2-oneO=C1C=C2C=CC=CC2=N12549.9Standard polar33892256
indol-2-oneO=C1C=C2C=CC=CC2=N11563.5Standard non polar33892256
indol-2-oneO=C1C=C2C=CC=CC2=N11455.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Indol-2-One GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f89-1900000000-e3622b0b439a6b49de842021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Indol-2-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 - Indol-2-One 10V, Positive-QTOFsplash10-001i-0900000000-3ee0f5a606d237c0df412021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indol-2-One 20V, Positive-QTOFsplash10-0f89-0900000000-935c4815e81549bf3d4d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indol-2-One 40V, Positive-QTOFsplash10-0fb9-9300000000-6c771720b00c470977d62021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indol-2-One 10V, Negative-QTOFsplash10-001i-0900000000-ddf5ec2fd679e8c548842021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indol-2-One 20V, Negative-QTOFsplash10-001i-0900000000-ddf5ec2fd679e8c548842021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Indol-2-One 40V, Negative-QTOFsplash10-001i-0900000000-f1a9bef473849b7c2b892021-10-12Wishart 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 ID10613893
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound17904787
PDB IDNot Available
ChEBI ID51630
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 ]