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Showing metabocard for Methylcyclopentane (HMDB0031542)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:43:57 UTC
Update Date2022-03-07 02:53:01 UTC
HMDB IDHMDB0031542
Secondary Accession Numbers
  • HMDB31542
Metabolite Identification
Common NameMethylcyclopentane
DescriptionMethylcyclopentane, also known as methylpentamethylene, belongs to the class of organic compounds known as cycloalkanes. These are saturated monocyclic hydrocarbons (with or without side chains). Methylcyclopentane has been detected, but not quantified, in celeriacs and celery stalks. This could make methylcyclopentane a potential biomarker for the consumption of these foods. At high amounts methylcyclopentane is a potentially toxic compound and central nervous system depression may occur, with symptoms such as weakness, dizziness, slow and shallow respiration, unconsciousness, and convulsions. Methylcyclopentane is a volatile component of petroleum distillates. Petroleum distillates are aspiration hazards and may cause pulmonary damage, central nervous system depression, and cardiac effects such as cardiac arrhythmias. They may also affect the blood, immune system, liver, and kidney. Volatile hydrocarbons are absorbed mainly through the lungs, and may also enter the body after ingestion via aspiration. Treatment is mainly symptomatic and supportive. Petroleum distillates are also irritating to the skin. Petroleum distillate poisoning may cause nausea, vomiting, cough, pulmonary irritation progressing to pulmonary edema, bloody sputum, and bronchial pneumonia. Gastric lavage, emesis, and the administration of activated charcoal should be avoided, as vomiting increases the risk of aspiration.
Structure
Data?1563862138
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031542 (Methylcyclopentane)


  Mrv1652305271900212D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
Download

3D MOL for HMDB0031542 (Methylcyclopentane)

HMDB0031542
     RDKit          3D
Methylcyclopentane
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.0665   -0.0400   -0.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6737   -0.4178    0.1663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2445   -0.5395   -1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6114   -0.4395   -0.3611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4024    0.7954    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0052    0.5823    1.0463 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0712    0.7604   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6310    0.2207    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5607   -0.9585   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7061   -1.4357    0.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1185    0.3672   -1.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1141   -1.4794   -1.5836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3050    0.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4304   -0.3400   -1.0800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3953    1.6855   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1659    0.8596    1.3036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0681    0.1289    2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5210    1.5554    1.0707 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
Download

3D SDF for HMDB0031542 (Methylcyclopentane)


  Mrv1652305271900212D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  1  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031542

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H12/c1-6-4-2-3-5-6/h6H,2-5H2,1H3

> <INCHI_KEY>
GDOPTJXRTPNYNR-UHFFFAOYSA-N

> <FORMULA>
C6H12

> <MOLECULAR_WEIGHT>
84.1595

> <EXACT_MASS>
84.093900384

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
11.150882417548582

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methylcyclopentane

> <ALOGPS_LOGP>
3.15

> <JCHEM_LOGP>
2.5098624213333336

> <ALOGPS_LOGS>
-3.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
27.5536

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.91e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylcyclopentane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031542 (Methylcyclopentane)

HMDB0031542
     RDKit          3D
Methylcyclopentane
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.0665   -0.0400   -0.2261 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6737   -0.4178    0.1663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2445   -0.5395   -1.0503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6114   -0.4395   -0.3611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4024    0.7954    0.4925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0052    0.5823    1.0463 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0712    0.7604   -0.9845 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6310    0.2207    0.6770 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5607   -0.9585   -0.6437 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7061   -1.4357    0.6357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1185    0.3672   -1.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1141   -1.4794   -1.5836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6745   -1.3050    0.3082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4304   -0.3400   -1.0800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3953    1.6855   -0.1577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1659    0.8596    1.3036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0681    0.1289    2.0704 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5210    1.5554    1.0707 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
  6 18  1  0
M  END
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PDB for HMDB0031542 (Methylcyclopentane)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    6                                                       
CONECT    6    1    4    5                                                  
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0031542 (Methylcyclopentane)

COMPND    HMDB0031542
HETATM    1  C1  UNL     1       2.066  -0.040  -0.226  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.674  -0.418   0.166  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.244  -0.539  -1.050  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.611  -0.439  -0.361  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.402   0.795   0.493  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.005   0.582   1.046  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.071   0.760  -0.984  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.631   0.221   0.677  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.561  -0.959  -0.644  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.706  -1.436   0.636  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.119   0.367  -1.684  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.114  -1.479  -1.584  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.674  -1.305   0.308  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.430  -0.340  -1.080  1.00  0.00           H  
HETATM   15  H9  UNL     1      -1.395   1.685  -0.158  1.00  0.00           H  
HETATM   16  H10 UNL     1      -2.166   0.860   1.304  1.00  0.00           H  
HETATM   17  H11 UNL     1      -0.068   0.129   2.070  1.00  0.00           H  
HETATM   18  H12 UNL     1       0.521   1.555   1.071  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    6   10
CONECT    3    4   11   12
CONECT    4    5   13   14
CONECT    5    6   15   16
CONECT    6   17   18
END
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SMILES for HMDB0031542 (Methylcyclopentane)

CC1CCCC1
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INCHI for HMDB0031542 (Methylcyclopentane)

InChI=1S/C6H12/c1-6-4-2-3-5-6/h6H,2-5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Methyl cyclopentaneChEBI
Methyl-cyclopentaneChEBI
MethylpentamethyleneChEBI
Chemical FormulaC6H12
Average Molecular Weight84.1595
Monoisotopic Molecular Weight84.093900384
IUPAC Namemethylcyclopentane
Traditional Namemethylcyclopentane
CAS Registry Number96-37-7
SMILES
CC1CCCC1
InChI Identifier
InChI=1S/C6H12/c1-6-4-2-3-5-6/h6H,2-5H2,1H3
InChI KeyGDOPTJXRTPNYNR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cycloalkanes. These are saturated monocyclic hydrocarbons (with or without side chains).
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassCycloalkanes
Direct ParentCycloalkanes
Alternative ParentsNot Available
Substituents
  • Cycloalkane
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-139.8 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogP3.37Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.049 g/LALOGPS
logP3.15ALOGPS
logP2.51ChemAxon
logS-3.2ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity27.55 m³·mol⁻¹ChemAxon
Polarizability11.15 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+116.38331661259
DarkChem[M-H]-109.73431661259
DeepCCS[M+H]+126.64330932474
DeepCCS[M-H]-124.64530932474
DeepCCS[M-2H]-160.07630932474
DeepCCS[M+Na]+134.59930932474
AllCCS[M+H]+116.732859911
AllCCS[M+H-H2O]+111.632859911
AllCCS[M+NH4]+121.532859911
AllCCS[M+Na]+122.932859911
AllCCS[M-H]-124.132859911
AllCCS[M+Na-2H]-127.932859911
AllCCS[M+HCOO]-132.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethylcyclopentaneCC1CCCC1694.9Standard polar33892256
MethylcyclopentaneCC1CCCC1612.3Standard non polar33892256
MethylcyclopentaneCC1CCCC1627.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Methylcyclopentane EI-B (Non-derivatized)splash10-0a4l-9000000000-f36947d92a09565016ad2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Methylcyclopentane CI-B (Non-derivatized)splash10-001i-9000000000-89652fbd27509594b6192017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Methylcyclopentane EI-B (Non-derivatized)splash10-0a4l-9000000000-f36947d92a09565016ad2018-05-18HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Methylcyclopentane CI-B (Non-derivatized)splash10-001i-9000000000-89652fbd27509594b6192018-05-18HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methylcyclopentane GC-MS (Non-derivatized) - 70eV, Positivesplash10-069u-9000000000-f20228dae0dda76bc5672017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Methylcyclopentane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-0a4l-9000000000-e94ad8098b4b70c9d7482014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 10V, Positive-QTOFsplash10-000i-9000000000-32d4c2667ea3fb16d0df2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 20V, Positive-QTOFsplash10-000i-9000000000-d818a8aa9bf254dadac52015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 40V, Positive-QTOFsplash10-0a4l-9000000000-df6a147e653036178f262015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 10V, Negative-QTOFsplash10-001i-9000000000-6d1754df5318b34cabe22015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 20V, Negative-QTOFsplash10-001i-9000000000-6d1754df5318b34cabe22015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 40V, Negative-QTOFsplash10-00lr-9000000000-f8ed5bb4f934bc89073f2015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 10V, Positive-QTOFsplash10-0a4r-9000000000-79a23acab097b8c24d752021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 20V, Positive-QTOFsplash10-0a4l-9000000000-deb6f40b714e47a3d1322021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 40V, Positive-QTOFsplash10-0006-9000000000-87fe95b8405e28cf90fc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 10V, Negative-QTOFsplash10-001i-9000000000-1fe2685b7f3004ca04a32021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 20V, Negative-QTOFsplash10-001i-9000000000-386a19febdb8857d4e222021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Methylcyclopentane 40V, Negative-QTOFsplash10-001i-9000000000-bea98e26b5e568f762382021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008152
KNApSAcK IDNot Available
Chemspider ID7024
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethylcyclopentane
METLIN IDNot Available
PubChem Compound7296
PDB IDNot Available
ChEBI ID88429
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. Sprengnether MM, Demerjian KL, Dransfield TJ, Clarke JS, Anderson JG, Donahue NM: Rate constants of nine C6-C9 alkanes with OH from 230 to 379 K: chemical tracers for [OH]. J Phys Chem A. 2009 Apr 30;113(17):5030-8. doi: 10.1021/jp810412m. [PubMed:19334733 ]
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  3. de Blas M, Navazo M, Alonso L, Durana N, Gomez MC, Iza J: Simultaneous indoor and outdoor on-line hourly monitoring of atmospheric volatile organic compounds in an urban building. The role of inside and outside sources. Sci Total Environ. 2012 Jun 1;426:327-35. doi: 10.1016/j.scitotenv.2012.04.003. Epub 2012 Apr 26. [PubMed:22542255 ]
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