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Showing metabocard for 2-Methyl-1,3-cyclohexadiene (HMDB0032395)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:49:35 UTC
Update Date2022-03-07 02:53:20 UTC
HMDB IDHMDB0032395
Secondary Accession Numbers
  • HMDB32395
Metabolite Identification
Common Name2-Methyl-1,3-cyclohexadiene
Description2-Methyl-1,3-cyclohexadiene, also known as 1,3-cyclohexadiene, 3-methyl or 4,5-dihydrotoluene, belongs to the class of organic compounds known as branched unsaturated hydrocarbons. These are hydrocarbons that contains one or more unsaturated carbon atoms, and an aliphatic branch. Based on a literature review very few articles have been published on 2-Methyl-1,3-cyclohexadiene.
Structure
Data?1563862258
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)


  Mrv0541 05061306292D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    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
    1.4289    0.0000    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
    1.4289    0.8250    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
    0.7145    1.2375    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  2  0  0  0  0
  6  4  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
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3D MOL for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

HMDB0032395
     RDKit          3D
2-Methyl-1,3-cyclohexadiene
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4280   -0.1570   -0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9623   -0.0354   -0.0429 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1775   -1.0473   -0.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2552   -1.0145   -0.2710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8771    0.2493    0.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9603    1.3286    0.4301 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327    1.2198    0.3534 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7551   -0.9857   -0.7783 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8651   -0.3464    0.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8459    0.8132   -0.5038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6810   -1.9858   -0.6096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5953   -1.1876   -1.3619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6969   -1.8677    0.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6999    0.5828   -0.5800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4623    0.0317    1.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4347    2.2944    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9341    2.1077    0.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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3D SDF for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)


  Mrv0541 05061306292D          

  7  7  0  0  0  0            999 V2000
    0.7145    2.0625    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
    1.4289    0.0000    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
    1.4289    0.8250    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
    0.7145    1.2375    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  2  0  0  0  0
  6  4  1  0  0  0  0
  7  1  1  0  0  0  0
  7  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0032395

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CCCC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H10/c1-7-5-3-2-4-6-7/h3,5-6H,2,4H2,1H3

> <INCHI_KEY>
XMWINMVFKPHMJB-UHFFFAOYSA-N

> <FORMULA>
C7H10

> <MOLECULAR_WEIGHT>
94.1543

> <EXACT_MASS>
94.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
11.646826972868931

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-methylcyclohexa-1,3-diene

> <ALOGPS_LOGP>
2.64

> <JCHEM_LOGP>
2.1869299483333333

> <ALOGPS_LOGS>
-1.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
34.1212

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.36e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-cyclohexadiene, 2-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

HMDB0032395
     RDKit          3D
2-Methyl-1,3-cyclohexadiene
 17 17  0  0  0  0  0  0  0  0999 V2000
    2.4280   -0.1570   -0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9623   -0.0354   -0.0429 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1775   -1.0473   -0.3196 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2552   -1.0145   -0.2710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8771    0.2493    0.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9603    1.3286    0.4301 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3327    1.2198    0.3534 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7551   -0.9857   -0.7783 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8651   -0.3464    0.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8459    0.8132   -0.5038 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6810   -1.9858   -0.6096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5953   -1.1876   -1.3619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6969   -1.8677    0.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6999    0.5828   -0.5800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4623    0.0317    1.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4347    2.2944    0.7340 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9341    2.1077    0.5980 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  7  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
M  END
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PDB for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

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       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -0.770   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   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
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    7                                                       
CONECT    7    1    5    6                                                  
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

COMPND    HMDB0032395
HETATM    1  C1  UNL     1       2.428  -0.157  -0.120  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.962  -0.035  -0.043  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.178  -1.047  -0.320  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.255  -1.015  -0.271  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.877   0.249   0.140  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.960   1.329   0.430  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.333   1.220   0.353  1.00  0.00           C  
HETATM    8  H1  UNL     1       2.755  -0.986  -0.778  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.865  -0.346   0.883  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.846   0.813  -0.504  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.681  -1.986  -0.610  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.595  -1.188  -1.362  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.697  -1.868   0.333  1.00  0.00           H  
HETATM   14  H7  UNL     1      -2.700   0.583  -0.580  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.462   0.032   1.115  1.00  0.00           H  
HETATM   16  H9  UNL     1      -1.435   2.294   0.734  1.00  0.00           H  
HETATM   17  H10 UNL     1       0.934   2.108   0.598  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    7
CONECT    3    4   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    7   16
CONECT    7   17
END
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SMILES for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

CC1=CCCC=C1
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INCHI for HMDB0032395 (2-Methyl-1,3-cyclohexadiene)

InChI=1S/C7H10/c1-7-5-3-2-4-6-7/h3,5-6H,2,4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3-Cyclohexadiene, 3-methylHMDB
4,5-DihydrotolueneHMDB
Chemical FormulaC7H10
Average Molecular Weight94.1543
Monoisotopic Molecular Weight94.07825032
IUPAC Name2-methylcyclohexa-1,3-diene
Traditional Name1,3-cyclohexadiene, 2-methyl-
CAS Registry Number1489-57-2
SMILES
CC1=CCCC=C1
InChI Identifier
InChI=1S/C7H10/c1-7-5-3-2-4-6-7/h3,5-6H,2,4H2,1H3
InChI KeyXMWINMVFKPHMJB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as branched unsaturated hydrocarbons. These are hydrocarbons that contains one or more unsaturated carbon atoms, and an aliphatic branch.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassBranched unsaturated hydrocarbons
Direct ParentBranched unsaturated hydrocarbons
Alternative Parents
Substituents
  • Branched unsaturated hydrocarbon
  • Cyclic olefin
  • Unsaturated aliphatic hydrocarbon
  • Olefin
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
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
Water Solubility1.36 g/LALOGPS
logP2.64ALOGPS
logP2.19ChemAxon
logS-1.8ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity34.12 m³·mol⁻¹ChemAxon
Polarizability11.65 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]+119.69731661259
DarkChem[M-H]-113.26131661259
DeepCCS[M+H]+123.40730932474
DeepCCS[M-H]-121.09530932474
DeepCCS[M-2H]-157.09630932474
DeepCCS[M+Na]+131.74730932474
AllCCS[M+H]+116.032859911
AllCCS[M+H-H2O]+110.832859911
AllCCS[M+NH4]+120.832859911
AllCCS[M+Na]+122.232859911
AllCCS[M-H]-119.032859911
AllCCS[M+Na-2H]-122.132859911
AllCCS[M+HCOO]-125.532859911

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. 4.09 minutes32390414
Predicted by Siyang on May 30, 202215.6884 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.0 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1943.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid539.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid231.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid421.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid278.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid516.1 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 Acid480.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)130.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1323.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid458.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid939.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid502.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid410.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate525.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA526.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water75.0 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methyl-1,3-cyclohexadieneCC1=CCCC=C1920.9Standard polar33892256
2-Methyl-1,3-cyclohexadieneCC1=CCCC=C1767.4Standard non polar33892256
2-Methyl-1,3-cyclohexadieneCC1=CCCC=C1765.8Semi standard non polar33892256
Spectra
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 IDFDB009823
KNApSAcK IDNot Available
Chemspider ID66519
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound73885
PDB IDNot Available
ChEBI IDNot Available
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. (). EAFUS: Everything Added to Food in the United States.. .