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Showing metabocard for 3-Methylcyclopentene (HMDB0031544)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:43:58 UTC
Update Date2022-03-07 02:53:01 UTC
HMDB IDHMDB0031544
Secondary Accession Numbers
  • HMDB31544
Metabolite Identification
Common Name3-Methylcyclopentene
Description3-Methylcyclopentene belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond. Based on a literature review a significant number of articles have been published on 3-Methylcyclopentene.
Structure
Data?1563862139
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031544 (3-Methylcyclopentene)


  Mrv0541 05061305592D          

  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  2  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
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3D MOL for HMDB0031544 (3-Methylcyclopentene)

HMDB0031544
     RDKit          3D
3-Methylcyclopentene
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.7399    0.1068   -0.1146 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5100   -0.1864    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3576    1.0036    0.8798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3348    1.0124   -0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2092   -0.1866   -0.8701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3891   -1.1432   -0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1785    1.0451    0.2492 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5230    0.0988   -1.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4735   -0.7015    0.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7490   -0.5949    1.6955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2240    1.7657    1.6208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964    1.7725   -0.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5769    0.0967   -1.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1972   -0.5413   -1.1303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9974   -1.7725    0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2088   -1.7751   -0.6985 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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3D SDF for HMDB0031544 (3-Methylcyclopentene)


  Mrv0541 05061305592D          

  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  2  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>
HMDB0031544

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1CCC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10/c1-6-4-2-3-5-6/h2,4,6H,3,5H2,1H3

> <INCHI_KEY>
CXOZQHPXKPDQGT-UHFFFAOYSA-N

> <FORMULA>
C6H10

> <MOLECULAR_WEIGHT>
82.1436

> <EXACT_MASS>
82.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
10.351941580735197

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylcyclopent-1-ene

> <ALOGPS_LOGP>
2.64

> <JCHEM_LOGP>
2.1479407646666666

> <ALOGPS_LOGS>
-2.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
28.6702

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentene, 3-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031544 (3-Methylcyclopentene)

HMDB0031544
     RDKit          3D
3-Methylcyclopentene
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.7399    0.1068   -0.1146 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5100   -0.1864    0.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3576    1.0036    0.8798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3348    1.0124   -0.0142 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2092   -0.1866   -0.8701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3891   -1.1432   -0.0406 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1785    1.0451    0.2492 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5230    0.0988   -1.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4735   -0.7015    0.1163 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7490   -0.5949    1.6955 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2240    1.7657    1.6208 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0964    1.7725   -0.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5769    0.0967   -1.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1972   -0.5413   -1.1303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9974   -1.7725    0.6264 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2088   -1.7751   -0.6985 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  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
  4 12  1  0
  5 13  1  0
  5 14  1  0
  6 15  1  0
  6 16  1  0
M  END
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PDB for HMDB0031544 (3-Methylcyclopentene)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         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 HMDB0031544 (3-Methylcyclopentene)

COMPND    HMDB0031544
HETATM    1  C1  UNL     1       1.740   0.107  -0.115  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.510  -0.186   0.715  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.358   1.004   0.880  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.335   1.012  -0.014  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.209  -0.187  -0.870  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.389  -1.143  -0.041  1.00  0.00           C  
HETATM    7  H1  UNL     1       2.179   1.045   0.249  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.523   0.099  -1.192  1.00  0.00           H  
HETATM    9  H3  UNL     1       2.473  -0.701   0.116  1.00  0.00           H  
HETATM   10  H4  UNL     1       0.749  -0.595   1.696  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.224   1.766   1.621  1.00  0.00           H  
HETATM   12  H6  UNL     1      -2.096   1.772  -0.101  1.00  0.00           H  
HETATM   13  H7  UNL     1      -0.577   0.097  -1.743  1.00  0.00           H  
HETATM   14  H8  UNL     1      -2.197  -0.541  -1.130  1.00  0.00           H  
HETATM   15  H9  UNL     1      -0.997  -1.773   0.626  1.00  0.00           H  
HETATM   16  H10 UNL     1       0.209  -1.775  -0.698  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3    6   10
CONECT    3    4    4   11
CONECT    4    5   12
CONECT    5    6   13   14
CONECT    6   15   16
END
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SMILES for HMDB0031544 (3-Methylcyclopentene)

CC1CCC=C1
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INCHI for HMDB0031544 (3-Methylcyclopentene)

InChI=1S/C6H10/c1-6-4-2-3-5-6/h2,4,6H,3,5H2,1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Methyl-1-cyclopenteneHMDB
3-Methyl-cyclopenteneHMDB
3-Methylcyclopentene-1HMDB
Chemical FormulaC6H10
Average Molecular Weight82.1436
Monoisotopic Molecular Weight82.07825032
IUPAC Name3-methylcyclopent-1-ene
Traditional Namecyclopentene, 3-methyl-
CAS Registry Number1120-62-3
SMILES
CC1CCC=C1
InChI Identifier
InChI=1S/C6H10/c1-6-4-2-3-5-6/h2,4,6H,3,5H2,1H3
InChI KeyCXOZQHPXKPDQGT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassOlefins
Direct ParentCycloalkenes
Alternative Parents
Substituents
  • Cycloalkene
  • Unsaturated aliphatic hydrocarbon
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point64.90 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility128.8 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP2.820 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.22 g/LALOGPS
logP2.64ALOGPS
logP2.15ChemAxon
logS-2.6ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.67 m³·mol⁻¹ChemAxon
Polarizability10.35 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]+116.05131661259
DarkChem[M-H]-109.80731661259
DeepCCS[M+H]+125.14530932474
DeepCCS[M-H]-122.99230932474
DeepCCS[M-2H]-158.85530932474
DeepCCS[M+Na]+133.29730932474
AllCCS[M+H]+114.832859911
AllCCS[M+H-H2O]+109.632859911
AllCCS[M+NH4]+119.632859911
AllCCS[M+Na]+121.032859911
AllCCS[M-H]-120.332859911
AllCCS[M+Na-2H]-124.132859911
AllCCS[M+HCOO]-128.332859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.61 minutes32390414
Predicted by Siyang on May 30, 202216.2015 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.58 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1870.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid607.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid246.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid450.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid342.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid623.2 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid580.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)242.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1328.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid466.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1204.1 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid489.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid423.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate612.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA529.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water100.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-MethylcyclopenteneCC1CCC=C1716.2Standard polar33892256
3-MethylcyclopenteneCC1CCC=C1607.5Standard non polar33892256
3-MethylcyclopenteneCC1CCC=C1607.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylcyclopentene GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-9000000000-0adcda652cc3a9a6ad8c2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylcyclopentene 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 - 3-Methylcyclopentene 10V, Positive-QTOFsplash10-001i-9000000000-cf05711c4699b5aa62f22016-06-20Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 20V, Positive-QTOFsplash10-001i-9000000000-045ee20b6a469a9dcc082016-06-20Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 40V, Positive-QTOFsplash10-05mo-9000000000-d23aff0d9c9638a6594a2016-06-20Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 10V, Negative-QTOFsplash10-001i-9000000000-fa5c9bf3f27c48b7b1612016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 20V, Negative-QTOFsplash10-001i-9000000000-fa5c9bf3f27c48b7b1612016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 40V, Negative-QTOFsplash10-00lr-9000000000-3336e1ffdeba1d0a176e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 10V, Negative-QTOFsplash10-001i-9000000000-6e756a4ab0e827bea25e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 20V, Negative-QTOFsplash10-001i-9000000000-6e756a4ab0e827bea25e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 40V, Negative-QTOFsplash10-00lr-9000000000-7db4c12c3ae0b6409b022021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 10V, Positive-QTOFsplash10-0536-9000000000-ad3bd38fdc55998aa7192021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 20V, Positive-QTOFsplash10-00kf-9000000000-9507b47ba7f9527c13022021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylcyclopentene 40V, Positive-QTOFsplash10-0pvu-9000000000-f7e58dfa227609407f682021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008154
KNApSAcK IDC00056472
Chemspider ID13625
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14263
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1509441
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .