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Showing metabocard for 3-Methyl-1-butene (HMDB0245923)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:58:12 UTC
Update Date2021-09-26 22:54:39 UTC
HMDB IDHMDB0245923
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Methyl-1-butene
Description3-Methyl-1-butene, also known as alpha-isoamylene or (CH3)2chch=ch2, belongs to the class of organic compounds known as unsaturated aliphatic hydrocarbons. These are aliphatic Hydrocarbons that contains one or more unsaturated carbon atoms. These compounds contain one or more double or triple bonds. 3-Methyl-1-butene has been detected, but not quantified in, sweet oranges (Citrus sinensis). This could make 3-methyl-1-butene a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 3-Methyl-1-butene. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-methyl-1-butene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Methyl-1-butene 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 HMDB0245923 (3-Methyl-1-butene)

  Mrv0541 02241205132D          

  5  4  0  0  0  0            999 V2000
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
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3D MOL for HMDB0245923 (3-Methyl-1-butene)

HMDB0245923
     RDKit          3D
3-Methyl-1-butene
 15 14  0  0  0  0  0  0  0  0999 V2000
    1.8012   -0.6090    0.9330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0846   -0.3138   -0.1234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3275    0.0678    0.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2097   -0.8959   -0.7158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5029    1.4609   -0.5262 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8288   -0.8865    0.8208 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3571   -0.5715    1.9023 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5134   -0.3439   -1.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705    0.0879    1.0762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1146   -1.8822   -0.2083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8739   -0.9364   -1.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2690   -0.6028   -0.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862    2.1259    0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391    1.8037   -0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2642    1.4958   -1.6070 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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3D SDF for HMDB0245923 (3-Methyl-1-butene)

  Mrv0541 02241205132D          

  5  4  0  0  0  0            999 V2000
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    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  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245923

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H10/c1-4-5(2)3/h4-5H,1H2,2-3H3

> <INCHI_KEY>
YHQXBTXEYZIYOV-UHFFFAOYSA-N

> <FORMULA>
C5H10

> <MOLECULAR_WEIGHT>
70.1329

> <EXACT_MASS>
70.07825032

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
9.321090773554001

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbut-1-ene

> <ALOGPS_LOGP>
2.30

> <JCHEM_LOGP>
2.225031672666667

> <ALOGPS_LOGS>
-2.43

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
24.7989

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.62e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyl-1-butene

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0245923 (3-Methyl-1-butene)

HMDB0245923
     RDKit          3D
3-Methyl-1-butene
 15 14  0  0  0  0  0  0  0  0999 V2000
    1.8012   -0.6090    0.9330 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0846   -0.3138   -0.1234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3275    0.0678    0.0288 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2097   -0.8959   -0.7158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5029    1.4609   -0.5262 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8288   -0.8865    0.8208 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3571   -0.5715    1.9023 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5134   -0.3439   -1.1268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705    0.0879    1.0762 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1146   -1.8822   -0.2083 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8739   -0.9364   -1.7643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2690   -0.6028   -0.6963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1862    2.1259    0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5391    1.8037   -0.3370 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2642    1.4958   -1.6070 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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PDB for HMDB0245923 (3-Methyl-1-butene)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   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
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0245923 (3-Methyl-1-butene)

COMPND    HMDB0245923
HETATM    1  C1  UNL     1       1.801  -0.609   0.933  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.085  -0.314  -0.123  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.328   0.068   0.029  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.210  -0.896  -0.716  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.503   1.461  -0.526  1.00  0.00           C  
HETATM    6  H1  UNL     1       2.829  -0.887   0.821  1.00  0.00           H  
HETATM    7  H2  UNL     1       1.357  -0.571   1.902  1.00  0.00           H  
HETATM    8  H3  UNL     1       1.513  -0.344  -1.127  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.670   0.088   1.076  1.00  0.00           H  
HETATM   10  H5  UNL     1      -1.115  -1.882  -0.208  1.00  0.00           H  
HETATM   11  H6  UNL     1      -0.874  -0.936  -1.764  1.00  0.00           H  
HETATM   12  H7  UNL     1      -2.269  -0.603  -0.696  1.00  0.00           H  
HETATM   13  H8  UNL     1       0.186   2.126   0.057  1.00  0.00           H  
HETATM   14  H9  UNL     1      -1.539   1.804  -0.337  1.00  0.00           H  
HETATM   15  H10 UNL     1      -0.264   1.496  -1.607  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    5    9
CONECT    4   10   11   12
CONECT    5   13   14   15
END
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SMILES for HMDB0245923 (3-Methyl-1-butene)

CC(C)C=C
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INCHI for HMDB0245923 (3-Methyl-1-butene)

InChI=1S/C5H10/c1-4-5(2)3/h4-5H,1H2,2-3H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(CH3)2CHCH=ch2ChEBI
2-Methyl-3-buteneChEBI
3-Methylbutene-1ChEBI
alpha-IsoamyleneChEBI
IsopenteneChEBI
IsopropylethyleneChEBI
VinylisopropylChEBI
a-IsoamyleneGenerator
Α-isoamyleneGenerator
3-Methyl-1-buteneChEBI
Chemical FormulaC5H10
Average Molecular Weight70.1329
Monoisotopic Molecular Weight70.07825032
IUPAC Name3-methylbut-1-ene
Traditional Name3-methyl-1-butene
CAS Registry NumberNot Available
SMILES
CC(C)C=C
InChI Identifier
InChI=1S/C5H10/c1-4-5(2)3/h4-5H,1H2,2-3H3
InChI KeyYHQXBTXEYZIYOV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as unsaturated aliphatic hydrocarbons. These are aliphatic Hydrocarbons that contains one or more unsaturated carbon atoms. These compounds contain one or more double or triple bonds.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassUnsaturated aliphatic hydrocarbons
Direct ParentUnsaturated aliphatic hydrocarbons
Alternative Parents
Substituents
  • Unsaturated aliphatic hydrocarbon
  • Olefin
  • Alkene
  • Acyclic olefin
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP2.3ALOGPS
logP2.23ChemAxon
logS-2.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity24.8 m³·mol⁻¹ChemAxon
Polarizability9.32 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
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 IDFDB005083
KNApSAcK IDNot Available
Chemspider ID10765
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11239
PDB IDNot Available
ChEBI ID77914
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1191551
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 ]