Showing metabocard for Isoprene (MMDBc0049865)

Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-04-29 22:45:05 UTC
Update Date2025-10-07 16:04:12 UTC
Metabolite IDMMDBc0049865
Metabolite Identification
Common NameIsoprene
DescriptionIsoprene is a non-methane hydrocarbon classified as a volatile organic compound (VOC) with the chemical formula C5H8. Its structure consists of a branched chain of five carbon atoms, featuring two double bonds, which contributes to its high reactivity and volatility. Isoprene plays a significant role in atmospheric chemistry, particularly in the formation of secondary organic aerosols (SOA) through photochemical oxidation and heterogeneous-phase reactions, with its contribution diminishing at elevated temperatures (PMID:41033624 ). It is the most emitted non-methane hydrocarbon into the atmosphere, and its oxidation products are crucial for the rapid formation and growth of new particles in the tropical upper troposphere (PMID:41022896 ). The understanding of isoprene oxidation pathways, particularly at low temperatures, remains limited (PMID:41022896 ). Additionally, isoprene serves as a fundamental building block for monoterpenes, which are significant in various biosynthetic pathways (PMID:41009805 ). Its reactivity is also notable in combustion processes, where it forms intermediate species during biofuel oxidation, and in atmospheric chemistry as it participates in the formation of reactive oxygen species (ROS) (PMID:40990432 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9ad0574938>


  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 #<Metabolite:0x00007f9ad0574938>

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 #<Metabolite:0x00007f9ad0574938>


  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>
MMDBc0049865

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f9ad0574938>

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 #<Metabolite:0x00007f9ad0574938>

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 #<Metabolite:0x00007f9ad0574938>

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 #<Metabolite:0x00007f9ad0574938>

CC(=C)C=C
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INCHI for #<Metabolite:0x00007f9ad0574938>

InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
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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
Molecular FormulaC5H8
Average Mass68.117
Monoisotopic Mass68.062600256
IUPAC Name2-methylbuta-1,3-diene
Traditional Nameisoprene
CAS Registry Number78-79-5
SMILES
CC(=C)C=C
InChI Identifier
InChI=1S/C5H8/c1-4-5(2)3/h4H,1-2H2,3H3
InChI KeyRRHGJUQNOFWUDK-UHFFFAOYSA-N