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Showing metabocard for Isoprene (HMDB0253673)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:28:30 UTC
Update Date2022-11-24 00:09:12 UTC
HMDB IDHMDB0253673
Secondary Accession NumbersNone
Metabolite Identification
Common NameIsoprene
DescriptionIsoprene, also known as 2-methylbutadiene or 2-methyldivinyl, 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. Isoprene has been detected, but not quantified in, a few different foods, such as carrots (Daucus carota ssp. sativus), sweet oranges (Citrus sinensis), and wild carrots (Daucus carota). This could make isoprene a potential biomarker for the consumption of these foods. Isoprene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Isoprene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Isoprene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Isoprene 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 HMDB0253673 (Isoprene)


  Mrv1652303202019012D          

  5  4  0  0  0  0            999 V2000
    0.1105    0.4125    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
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  2  5  1  0  0  0  0
M  END
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3D MOL for HMDB0253673 (Isoprene)

HMDB0253673
     RDKit          3D
ISOPRENE
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.8305   -0.4478    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0169    0.5772    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4017    0.3617   -0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580    1.3671   -0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8680   -1.0627   -0.1551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9051   -0.3307    0.3486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4379   -1.4451    0.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4101    1.5935    0.2540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8812    2.3625    0.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2955    1.1526   -0.2276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5958   -1.6340    0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3485   -1.4568   -1.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9519   -1.0376   -0.2630 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  3
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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3D SDF for HMDB0253673 (Isoprene)


  Mrv1652303202019012D          

  5  4  0  0  0  0            999 V2000
    0.1105    0.4125    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
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  2  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253673

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3

> <INCHI_KEY>
RRHGJUQNOFWUDK-UHFFFAOYSA-N

> <FORMULA>
C5H8

> <MOLECULAR_WEIGHT>
68.117

> <EXACT_MASS>
68.062600256

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.576581738168763

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.22

> <JCHEM_LOGP>
1.8773858616666663

> <ALOGPS_LOGS>
-1.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
24.5764

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isoprene

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253673 (Isoprene)

HMDB0253673
     RDKit          3D
ISOPRENE
 13 12  0  0  0  0  0  0  0  0999 V2000
    1.8305   -0.4478    0.2095 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0169    0.5772    0.1569 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4017    0.3617   -0.0296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580    1.3671   -0.0884 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8680   -1.0627   -0.1551 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9051   -0.3307    0.3486 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4379   -1.4451    0.1134 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4101    1.5935    0.2540 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8812    2.3625    0.0056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2955    1.1526   -0.2276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5958   -1.6340    0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3485   -1.4568   -1.0649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9519   -1.0376   -0.2630 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  3
  3  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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PDB for HMDB0253673 (Isoprene)

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    5                                                  
CONECT    3    2    4                                                       
CONECT    4    3                                                            
CONECT    5    2                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0253673 (Isoprene)

COMPND    HMDB0253673
HETATM    1  C1  UNL     1       1.831  -0.448   0.209  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.017   0.577   0.157  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.402   0.362  -0.030  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.258   1.367  -0.088  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.868  -1.063  -0.155  1.00  0.00           C  
HETATM    6  H1  UNL     1       2.905  -0.331   0.349  1.00  0.00           H  
HETATM    7  H2  UNL     1       1.438  -1.445   0.113  1.00  0.00           H  
HETATM    8  H3  UNL     1       1.410   1.594   0.254  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.881   2.363   0.006  1.00  0.00           H  
HETATM   10  H5  UNL     1      -2.296   1.153  -0.228  1.00  0.00           H  
HETATM   11  H6  UNL     1      -0.596  -1.634   0.741  1.00  0.00           H  
HETATM   12  H7  UNL     1      -0.349  -1.457  -1.065  1.00  0.00           H  
HETATM   13  H8  UNL     1      -1.952  -1.038  -0.263  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    4    5
CONECT    4    9   10
CONECT    5   11   12   13
END
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SMILES for HMDB0253673 (Isoprene)

CC(=C)C=C
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INCHI for HMDB0253673 (Isoprene)

InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Methyl-1,3-butadieneChEBI
2-MethylbutadieneChEBI
2-MethyldivinylChEBI
beta-MethylbivinylChEBI
CH2=C(CH3)CH=ch2ChEBI
IsopentadieneChEBI
IsoprenChEBI
IsoprenoChEBI
IsoterpeneChEBI
b-MethylbivinylGenerator
Β-methylbivinylGenerator
Chemical FormulaC5H8
Average Molecular Weight68.117
Monoisotopic Molecular Weight68.062600256
IUPAC Name2-methylbuta-1,3-diene
Traditional Nameisoprene
CAS Registry NumberNot Available
SMILES
CC(=C)C=C
InChI Identifier
InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
InChI KeyRRHGJUQNOFWUDK-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
  • Alkadiene
  • Unsaturated aliphatic hydrocarbon
  • Olefin
  • Acyclic olefin
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
Process
Naturally occurring process
Role
Biological role
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
logP2.22ALOGPS
logP1.88ChemAxon
logS-1.6ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity24.58 m³·mol⁻¹ChemAxon
Polarizability8.58 ųChemAxon
Number of Rings0ChemAxon
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]+119.6930932474
DeepCCS[M-H]-117.5630932474
DeepCCS[M-2H]-153.35630932474
DeepCCS[M+Na]+127.86330932474
AllCCS[M+H]+117.232859911
AllCCS[M+H-H2O]+112.632859911
AllCCS[M+NH4]+121.632859911
AllCCS[M+Na]+122.832859911
AllCCS[M-H]-125.532859911
AllCCS[M+Na-2H]-131.032859911
AllCCS[M+HCOO]-137.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ISOPRENECC(=C)C=C608.6Standard polar33892256
ISOPRENECC(=C)C=C502.8Standard non polar33892256
ISOPRENECC(=C)C=C492.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Isoprene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2020-06-30Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Isoprene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
MSMass Spectrum (Electron Ionization)splash10-014i-9000000000-bcc7aa57f0fa0fd9d3992014-09-20Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 10V, Positive-QTOFsplash10-014i-9000000000-aa7bf6693faf53f2c9f82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 20V, Positive-QTOFsplash10-014i-9000000000-79f5e8913a6e3948a9252016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 40V, Positive-QTOFsplash10-0udi-9000000000-cc71ad3e01e005b392f42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 10V, Negative-QTOFsplash10-014i-9000000000-c4e0cc5173528ae70b452016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 20V, Negative-QTOFsplash10-014i-9000000000-748a9309c1a76a36f5822016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 40V, Negative-QTOFsplash10-0uxr-9000000000-b24db55f64156fae0d1d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 10V, Positive-QTOFsplash10-014i-9000000000-13c3d4b2254b96312f2f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 20V, Positive-QTOFsplash10-014i-9000000000-182e8f0f63d0901250e72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 40V, Positive-QTOFsplash10-0udi-9000000000-7b7c61918e48120c38a52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 10V, Negative-QTOFsplash10-014i-9000000000-87c1aff470916cc072392021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 20V, Negative-QTOFsplash10-014i-9000000000-87c1aff470916cc072392021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Isoprene 40V, Negative-QTOFsplash10-0gb9-9000000000-7033f85bf44b5b1856d12021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
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 IDFDB005121
KNApSAcK IDC00046784
Chemspider ID6309
KEGG Compound IDC16521
BioCyc IDCPD-9436
BiGG IDNot Available
Wikipedia LinkIsoprene
METLIN IDNot Available
PubChem Compound6557
PDB IDNot Available
ChEBI ID35194
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1252691
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 ]