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Showing metabocard for Indene (HMDB0253451)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 11:53:52 UTC
Update Date2021-09-26 23:06:41 UTC
HMDB IDHMDB0253451
Secondary Accession NumbersNone
Metabolite Identification
Common NameIndene
DescriptionIndene, also known as inden or indonaphthene, belongs to the class of organic compounds known as indenes and isoindenes. Indenes and isoindenes are compounds containing an indene moiety(which consists of a cyclopentadiene fused to a benzene ring), or a isoindene moiety (which consists of a cyclopentadiene fused to cyclohexadiene ring). Based on a literature review a significant number of articles have been published on Indene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Indene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Indene 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 HMDB0253451 (Indene)


  Mrv0541 02231216282D          

  9 10  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    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  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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
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3D MOL for HMDB0253451 (Indene)

HMDB0253451
     RDKit          3D
Indene
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.3284    0.3950    0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4281    1.3472    0.0215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1005    0.7369   -0.0304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1684    1.3336   -0.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2566    0.5053   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1406   -0.8631   -0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9031   -1.4234    0.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2425   -0.6209    0.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6874   -0.9333    0.1698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3984    0.6224    0.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5917    2.4340   -0.0303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2458    2.4231   -0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2348    0.9795   -0.2631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0349   -1.4854   -0.1081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7458   -2.4796    0.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0311   -1.4722   -0.7432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9222   -1.4993    1.0924 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  1  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
  9 17  1  0
M  END
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3D SDF for HMDB0253451 (Indene)


  Mrv0541 02231216282D          

  9 10  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
    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  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
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  1  9  1  0  0  0  0
  4  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253451

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C=CC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C9H8/c1-2-5-9-7-3-6-8(9)4-1/h1-6H,7H2

> <INCHI_KEY>
YBYIRNPNPLQARY-UHFFFAOYSA-N

> <FORMULA>
C9H8

> <MOLECULAR_WEIGHT>
116.1598

> <EXACT_MASS>
116.062600256

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
13.3810167737891

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1H-indene

> <ALOGPS_LOGP>
3.04

> <JCHEM_LOGP>
2.7017097003333337

> <ALOGPS_LOGS>
-3.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
19.11316497402911

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
40.0558

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.68e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
indene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0253451 (Indene)

HMDB0253451
     RDKit          3D
Indene
 17 18  0  0  0  0  0  0  0  0999 V2000
    2.3284    0.3950    0.1354 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4281    1.3472    0.0215 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1005    0.7369   -0.0304 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1684    1.3336   -0.1480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2566    0.5053   -0.1717 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1406   -0.8631   -0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9031   -1.4234    0.0281 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2425   -0.6209    0.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6874   -0.9333    0.1698 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3984    0.6224    0.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5917    2.4340   -0.0303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2458    2.4231   -0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2348    0.9795   -0.2631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0349   -1.4854   -0.1081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7458   -2.4796    0.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0311   -1.4722   -0.7432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9222   -1.4993    1.0924 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  1  1  0
  8  3  1  0
  1 10  1  0
  2 11  1  0
  4 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  9 16  1  0
  9 17  1  0
M  END
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PDB for HMDB0253451 (Indene)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
CONECT    1    2    9                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8    1    4                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   20    0
END
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3D PDB for HMDB0253451 (Indene)

COMPND    HMDB0253451
HETATM    1  C1  UNL     1       2.328   0.395   0.135  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.428   1.347   0.022  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.100   0.737  -0.030  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.168   1.334  -0.148  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.257   0.505  -0.172  1.00  0.00           C  
HETATM    6  C6  UNL     1      -2.141  -0.863  -0.085  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.903  -1.423   0.028  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.242  -0.621   0.057  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.687  -0.933   0.170  1.00  0.00           C  
HETATM   10  H1  UNL     1       3.398   0.622   0.192  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.592   2.434  -0.030  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.246   2.423  -0.216  1.00  0.00           H  
HETATM   13  H4  UNL     1      -3.235   0.980  -0.263  1.00  0.00           H  
HETATM   14  H5  UNL     1      -3.035  -1.485  -0.108  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.746  -2.480   0.099  1.00  0.00           H  
HETATM   16  H7  UNL     1       2.031  -1.472  -0.743  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.922  -1.499   1.092  1.00  0.00           H  
CONECT    1    2    2    9   10
CONECT    2    3   11
CONECT    3    4    4    8
CONECT    4    5   12
CONECT    5    6    6   13
CONECT    6    7   14
CONECT    7    8    8   15
CONECT    8    9
CONECT    9   16   17
END
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SMILES for HMDB0253451 (Indene)

C1C=CC2=CC=CC=C12
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INCHI for HMDB0253451 (Indene)

InChI=1S/C9H8/c1-2-5-9-7-3-6-8(9)4-1/h1-6H,7H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
IndenChEBI
IndonaphtheneChEBI
Chemical FormulaC9H8
Average Molecular Weight116.1598
Monoisotopic Molecular Weight116.062600256
IUPAC Name1H-indene
Traditional Nameindene
CAS Registry NumberNot Available
SMILES
C1C=CC2=CC=CC=C12
InChI Identifier
InChI=1S/C9H8/c1-2-5-9-7-3-6-8(9)4-1/h1-6H,7H2
InChI KeyYBYIRNPNPLQARY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as indenes and isoindenes. Indenes and isoindenes are compounds containing an indene moiety(which consists of a cyclopentadiene fused to a benzene ring), or a isoindene moiety (which consists of a cyclopentadiene fused to cyclohexadiene ring).
KingdomOrganic compounds
Super ClassBenzenoids
ClassIndenes and isoindenes
Sub ClassNot Available
Direct ParentIndenes and isoindenes
Alternative Parents
Substituents
  • Indene
  • Aromatic hydrocarbon
  • Polycyclic hydrocarbon
  • Cyclic olefin
  • Unsaturated hydrocarbon
  • Olefin
  • Hydrocarbon
  • Aromatic homopolycyclic compound
Molecular FrameworkAromatic homopolycyclic 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
logP3.04ALOGPS
logP2.7ChemAxon
logS-3.1ALOGPS
pKa (Strongest Acidic)19.11ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity40.06 m³·mol⁻¹ChemAxon
Polarizability13.38 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]-158.25730932474
DeepCCS[M+Na]+133.11630932474
AllCCS[M+H]+123.732859911
AllCCS[M+H-H2O]+118.832859911
AllCCS[M+NH4]+128.332859911
AllCCS[M+Na]+129.632859911
AllCCS[M-H]-119.332859911
AllCCS[M+Na-2H]-120.832859911
AllCCS[M+HCOO]-122.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IndeneC1C=CC2=CC=CC=C121475.7Standard polar33892256
IndeneC1C=CC2=CC=CC=C121019.1Standard non polar33892256
IndeneC1C=CC2=CC=CC=C121043.9Semi standard non polar33892256
Spectra
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 IDC00013549
Chemspider ID6949
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIndene
METLIN IDNot Available
PubChem Compound7219
PDB IDNot Available
ChEBI ID41921
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1251321
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 ]