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Showing metabocard for Dicyclopentadiene (HMDB0251216)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 08:32:48 UTC
Update Date2021-09-26 23:03:05 UTC
HMDB IDHMDB0251216
Secondary Accession NumbersNone
Metabolite Identification
Common NameDicyclopentadiene
DescriptionDICYCLOPENTADIENE belongs to the class of organic compounds known as polycyclic hydrocarbons. These are polycyclic organic compounds made up only of carbon and hydrogen atoms. Based on a literature review a significant number of articles have been published on DICYCLOPENTADIENE. This compound has been identified in human blood as reported by (PMID: 31557052 ). Dicyclopentadiene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Dicyclopentadiene 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 HMDB0251216 (Dicyclopentadiene)


  Mrv1652304051723392D          

 10 12  0  0  0  0            999 V2000
   -0.7846    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5082    0.4125    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
    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
   -0.0000    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  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  1 10  1  0  0  0  0
  4 10  1  0  0  0  0
M  END
Download

3D MOL for HMDB0251216 (Dicyclopentadiene)

HMDB0251216
     RDKit          3D
Dicyclopentadiene
 22 24  0  0  0  0  0  0  0  0999 V2000
    2.2951    0.0442   -0.3590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5990    1.1005    0.0313 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3745    0.7656    0.7583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8580    1.2385    0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0941    0.6234    0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1061   -0.6749    0.3605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8507   -0.9659   -0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7481    0.3250   -1.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2800   -0.7386    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6045   -1.1876    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2425    0.0693   -0.9172 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    2.1294   -0.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3884    1.0786    1.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9260    2.2742   -0.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8733    1.1049    1.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8435   -1.4196    0.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -1.8602   -0.9492 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2307    0.4194   -1.6869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6109    0.4427   -1.8657 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0614   -1.1495    1.6013 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4900   -1.9092   -0.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2178   -1.7100    0.8432 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  2  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10  1  1  0
  9  3  1  0
  8  4  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 10 22  1  0
M  END
Download

3D SDF for HMDB0251216 (Dicyclopentadiene)


  Mrv1652304051723392D          

 10 12  0  0  0  0            999 V2000
   -0.7846    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    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
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5082    0.4125    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
    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
   -0.0000    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  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  5  9  1  0  0  0  0
  7 10  1  0  0  0  0
  1 10  1  0  0  0  0
  4 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0251216

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C=CC2C3CC(C=C3)C12

> <INCHI_IDENTIFIER>
InChI=1S/C10H12/c1-2-9-7-4-5-8(6-7)10(9)3-1/h1-2,4-5,7-10H,3,6H2

> <INCHI_KEY>
HECLRDQVFMWTQS-UHFFFAOYSA-N

> <FORMULA>
C10H12

> <MOLECULAR_WEIGHT>
132.206

> <EXACT_MASS>
132.093900386

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.394693119226957

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
tricyclo[5.2.1.0^{2,6}]deca-3,8-diene

> <ALOGPS_LOGP>
2.64

> <JCHEM_LOGP>
2.164193256666667

> <ALOGPS_LOGS>
-3.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
44.4292

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.35e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
tricyclo[5.2.1.0^{2,6}]deca-3,8-diene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0251216 (Dicyclopentadiene)

HMDB0251216
     RDKit          3D
Dicyclopentadiene
 22 24  0  0  0  0  0  0  0  0999 V2000
    2.2951    0.0442   -0.3590 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5990    1.1005    0.0313 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3745    0.7656    0.7583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8580    1.2385    0.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0941    0.6234    0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1061   -0.6749    0.3605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8507   -0.9659   -0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7481    0.3250   -1.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2800   -0.7386    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6045   -1.1876    0.0704 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2425    0.0693   -0.9172 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    2.1294   -0.1956 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3884    1.0786    1.8171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9260    2.2742   -0.1960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8733    1.1049    1.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8435   -1.4196    0.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8254   -1.8602   -0.9492 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2307    0.4194   -1.6869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6109    0.4427   -1.8657 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0614   -1.1495    1.6013 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4900   -1.9092   -0.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2178   -1.7100    0.8432 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  2  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10  1  1  0
  9  3  1  0
  8  4  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  4 14  1  0
  5 15  1  0
  6 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
 10 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0251216 (Dicyclopentadiene)

HEADER    PROTEIN                                 05-APR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-APR-17         0                                  
HETATM    1  C   UNK     0      -1.465   2.016   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.465  -0.476   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.949   0.770   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
HETATM    8  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   10                                                  
CONECT    8    7    9                                                       
CONECT    9    8    5                                                       
CONECT   10    7    1    4                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   24    0
END
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3D PDB for HMDB0251216 (Dicyclopentadiene)

COMPND    HMDB0251789
HETATM    1  C1  UNL     1      -1.722   0.926   0.791  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.854   1.491  -0.012  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.313   0.501  -1.001  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.185   0.492  -0.930  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.527   0.897   0.486  1.00  0.00           C  
HETATM    6  C6  UNL     1       0.958  -0.047   1.229  1.00  0.00           C  
HETATM    7  C7  UNL     1       0.528  -1.189   0.383  1.00  0.00           C  
HETATM    8  C8  UNL     1       1.528  -1.001  -0.779  1.00  0.00           C  
HETATM    9  C9  UNL     1      -0.729  -0.823  -0.374  1.00  0.00           C  
HETATM   10  C10 UNL     1      -1.898  -0.508   0.475  1.00  0.00           C  
HETATM   11  H1  UNL     1      -2.250   1.425   1.587  1.00  0.00           H  
HETATM   12  H2  UNL     1      -0.540   2.523  -0.003  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.724   0.655  -1.995  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.726   0.999  -1.687  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.108   1.769   0.757  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.835   0.028   2.297  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.555  -2.153   0.825  1.00  0.00           H  
HETATM   18  H8  UNL     1       2.556  -1.124  -0.429  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.243  -1.578  -1.653  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.913  -1.561  -1.176  1.00  0.00           H  
HETATM   21  H11 UNL     1      -2.816  -0.579  -0.168  1.00  0.00           H  
HETATM   22  H12 UNL     1      -1.992  -1.142   1.377  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4    9   13
CONECT    4    5    8   14
CONECT    5    6    6   15
CONECT    6    7   16
CONECT    7    8    9   17
CONECT    8   18   19
CONECT    9   10   20
CONECT   10   21   22
END
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SMILES for HMDB0251216 (Dicyclopentadiene)

C1C=CC2C3CC(C=C3)C12
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INCHI for HMDB0251216 (Dicyclopentadiene)

InChI=1S/C10H12/c1-2-9-7-4-5-8(6-7)10(9)3-1/h1-2,4-5,7-10H,3,6H2
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC10H12
Average Molecular Weight132.206
Monoisotopic Molecular Weight132.093900386
IUPAC Nametricyclo[5.2.1.0^{2,6}]deca-3,8-diene
Traditional Nametricyclo[5.2.1.0^{2,6}]deca-3,8-diene
CAS Registry NumberNot Available
SMILES
C1C=CC2C3CC(C=C3)C12
InChI Identifier
InChI=1S/C10H12/c1-2-9-7-4-5-8(6-7)10(9)3-1/h1-2,4-5,7-10H,3,6H2
InChI KeyHECLRDQVFMWTQS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as polycyclic hydrocarbons. These are polycyclic organic compounds made up only of carbon and hydrogen atoms.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassPolycyclic hydrocarbons
Sub ClassNot Available
Direct ParentPolycyclic hydrocarbons
Alternative Parents
Substituents
  • Polycyclic hydrocarbon
  • Cyclic olefin
  • Unsaturated aliphatic hydrocarbon
  • Unsaturated hydrocarbon
  • Olefin
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic 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
logP2.64ALOGPS
logP2.16ChemAxon
logS-3.8ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity44.43 m³·mol⁻¹ChemAxon
Polarizability15.39 ųChemAxon
Number of Rings3ChemAxon
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-2H]-168.86230932474
DeepCCS[M+Na]+144.2230932474
AllCCS[M+H]+128.532859911
AllCCS[M+H-H2O]+123.832859911
AllCCS[M+NH4]+132.932859911
AllCCS[M+Na]+134.232859911
AllCCS[M-H]-130.232859911
AllCCS[M+Na-2H]-131.132859911
AllCCS[M+HCOO]-132.232859911

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Dicyclopentadiene GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-9700000000-af956563a3b9f96f6d5c2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dicyclopentadiene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dicyclopentadiene 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 - Dicyclopentadiene 10V, Positive-QTOFsplash10-001i-0900000000-bd143053aea75038158b2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dicyclopentadiene 20V, Positive-QTOFsplash10-001l-5900000000-8c61e46b3b80e21807e82021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dicyclopentadiene 40V, Positive-QTOFsplash10-05o0-5900000000-ce265f1e677982e6c5a02021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dicyclopentadiene 10V, Negative-QTOFsplash10-001i-0900000000-b6dbb79105fa765a1a392021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dicyclopentadiene 20V, Negative-QTOFsplash10-001i-0900000000-b6dbb79105fa765a1a392021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dicyclopentadiene 40V, Negative-QTOFsplash10-00o0-0900000000-b85615686b533cf2e59b2021-10-12Wishart 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 ID6247
KEGG Compound IDC14411
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6492
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1042261
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 ]