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Showing metabocard for Cyclohexene (HMDB0250655)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:45:02 UTC
Update Date2021-09-26 23:02:15 UTC
HMDB IDHMDB0250655
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclohexene
Descriptioncyclohexene, also known as tetrahydrobenzene, belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond. cyclohexene is possibly neutral. A cycloalkene that is cylohexane with a single double bond. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclohexene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclohexene 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 HMDB0250655 (Cyclohexene)


  Mrv1533004171514082D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  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
  1  6  1  0  0  0  0
M  END
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3D MOL for HMDB0250655 (Cyclohexene)

HMDB0250655
     RDKit          3D
Cyclohexene
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.0414   -1.1289    0.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2245   -1.4801    0.0667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3372   -0.5161    0.2062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9709    0.9110   -0.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4512    1.0705   -0.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    0.2886    0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8146   -1.8560    0.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4754   -2.5473   -0.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7558   -0.6117    1.2500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -0.8453   -0.4678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1134    1.5701    0.7925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158    1.2857   -0.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5930    0.5971   -1.5695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7091    2.1292   -0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4234    0.5318    0.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2526    0.6014    1.4167 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  1  0
  6  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 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 HMDB0250655 (Cyclohexene)


  Mrv1533004171514082D          

  6  6  0  0  0  0            999 V2000
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  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
  1  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250655

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CCC=CC1

> <INCHI_IDENTIFIER>
InChI=1S/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2

> <INCHI_KEY>
HGCIXCUEYOPUTN-UHFFFAOYSA-N

> <FORMULA>
C6H10

> <MOLECULAR_WEIGHT>
82.146

> <EXACT_MASS>
82.078250322

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.339144059192408

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclohexene

> <ALOGPS_LOGP>
2.77

> <JCHEM_LOGP>
2.305490333333333

> <ALOGPS_LOGS>
-2.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
28.7226

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.06e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclohexene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0250655 (Cyclohexene)

HMDB0250655
     RDKit          3D
Cyclohexene
 16 16  0  0  0  0  0  0  0  0999 V2000
    1.0414   -1.1289    0.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2245   -1.4801    0.0667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3372   -0.5161    0.2062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9709    0.9110   -0.0936 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4512    1.0705   -0.5592 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819    0.2886    0.3696 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8146   -1.8560    0.0335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4754   -2.5473   -0.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7558   -0.6117    1.2500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1741   -0.8453   -0.4678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1134    1.5701    0.7925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6158    1.2857   -0.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5930    0.5971   -1.5695 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7091    2.1292   -0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4234    0.5318    0.0644 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2526    0.6014    1.4167 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  1  0
  6  1  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  3 10  1  0
  4 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 HMDB0250655 (Cyclohexene)

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0250655 (Cyclohexene)

COMPND    HMDB0250655
HETATM    1  C1  UNL     1       1.041  -1.129   0.139  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.224  -1.480   0.067  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.337  -0.516   0.206  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.971   0.911  -0.094  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.451   1.071  -0.559  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.382   0.289   0.370  1.00  0.00           C  
HETATM    7  H1  UNL     1       1.815  -1.856   0.034  1.00  0.00           H  
HETATM    8  H2  UNL     1      -0.475  -2.547  -0.108  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.756  -0.612   1.250  1.00  0.00           H  
HETATM   10  H4  UNL     1      -2.174  -0.845  -0.468  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.113   1.570   0.793  1.00  0.00           H  
HETATM   12  H6  UNL     1      -1.616   1.286  -0.939  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.593   0.597  -1.569  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.709   2.129  -0.602  1.00  0.00           H  
HETATM   15  H9  UNL     1       2.423   0.532   0.064  1.00  0.00           H  
HETATM   16  H10 UNL     1       1.253   0.601   1.417  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    9   10
CONECT    4    5   11   12
CONECT    5    6   13   14
CONECT    6   15   16
END
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SMILES for HMDB0250655 (Cyclohexene)

C1CCC=CC1
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INCHI for HMDB0250655 (Cyclohexene)

InChI=1S/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
1,2,3,4-TetrahydrobenzeneChEBI
1-CyclohexeneChEBI
3,4,5,6-TetrahydrobenzeneChEBI
Benzene tetrahydrideChEBI
BenzenetetrahydrideChEBI
Cyclohex-1-eneChEBI
TetrahydrobenzeneChEBI
ZyklohexenChEBI
Chemical FormulaC6H10
Average Molecular Weight82.146
Monoisotopic Molecular Weight82.078250322
IUPAC Namecyclohexene
Traditional Namecyclohexene
CAS Registry NumberNot Available
SMILES
C1CCC=CC1
InChI Identifier
InChI=1S/C6H10/c1-2-4-6-5-3-1/h1-2H,3-6H2
InChI KeyHGCIXCUEYOPUTN-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 Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP2.77ALOGPS
logP2.31ChemAxon
logS-2.9ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity28.72 m³·mol⁻¹ChemAxon
Polarizability10.34 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
DeepCCS[M+H]+123.33630932474
DeepCCS[M-H]-121.44130932474
DeepCCS[M-2H]-156.8930932474
DeepCCS[M+Na]+131.35130932474
AllCCS[M+H]+117.732859911
AllCCS[M+H-H2O]+112.532859911
AllCCS[M+NH4]+122.632859911
AllCCS[M+Na]+124.032859911
AllCCS[M-H]-121.532859911
AllCCS[M+Na-2H]-125.332859911
AllCCS[M+HCOO]-129.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202215.6952 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.2 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1862.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid557.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid234.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid436.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid358.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid587.0 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 Acid543.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)244.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1362.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid444.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1162.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid507.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid430.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate669.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA532.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water90.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclohexeneC1CCC=CC1846.7Standard polar33892256
CyclohexeneC1CCC=CC1672.9Standard non polar33892256
CyclohexeneC1CCC=CC1679.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclohexene GC-MS (Non-derivatized) - 70eV, Positivesplash10-003u-9000000000-2701e6bcef123224e0672021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclohexene 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 - Cyclohexene 10V, Positive-QTOFsplash10-001i-9000000000-0c64edb7cae17f3a1ee32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 20V, Positive-QTOFsplash10-001i-9000000000-2f334f4f459d942b0e712016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 40V, Positive-QTOFsplash10-0006-9000000000-e4690b818f6a15dc5f1e2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 10V, Negative-QTOFsplash10-001i-9000000000-a3c25e45deb5564d9c4a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 20V, Negative-QTOFsplash10-001i-9000000000-a3c25e45deb5564d9c4a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 40V, Negative-QTOFsplash10-001i-9000000000-85ebc40434e0cdb912352016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 10V, Positive-QTOFsplash10-001i-9000000000-399fb6fecf4ce54a943b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 20V, Positive-QTOFsplash10-0a4l-9000000000-585958ce6b2a00df1c232021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 40V, Positive-QTOFsplash10-052r-9000000000-7abb27ad7204e6308c492021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 10V, Negative-QTOFsplash10-001i-9000000000-6e756a4ab0e827bea25e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 20V, Negative-QTOFsplash10-001i-9000000000-6e756a4ab0e827bea25e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclohexene 40V, Negative-QTOFsplash10-001i-9000000000-434caa5f57e5756b212c2021-10-12Wishart 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyclohexene
METLIN IDNot Available
PubChem Compound8079
PDB IDNot Available
ChEBI ID36404
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 ]