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Showing metabocard for Cyclopentadiene (HMDB0061878)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2014-10-08 15:56:26 UTC
Update Date2022-03-07 03:17:49 UTC
HMDB IDHMDB0061878
Secondary Accession Numbers
  • HMDB61878
Metabolite Identification
Common NameCyclopentadiene
DescriptionCyclopentadiene, also known as HCp or pentole, belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond. Cyclopentadiene is an extremely weak acidic (essentially neutral) compound (based on its pKa). Diels–Alder reactions Cyclopentadiene is a highly reactive diene in the Diels–Alder reaction because minimal distortion of the diene is required to achieve the envelope geometry of the transition state compared to other dienes. This colorless liquid has a strong and unpleasant odor. This dimer can be restored by heating to give the monomer. Metallocenes and related cyclopentadienyl derivatives have been heavily investigated and represent a cornerstone of organometallic chemistry owing to their high stability. It was the starting material in Leo Paquette's 1982 synthesis of dodecahedrane.
Structure
Data?1589217815
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0061878 (Cyclopentadiene)

  Mrv1652304272018432D          

  5  5  0  0  0  0            999 V2000
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
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3D MOL for HMDB0061878 (Cyclopentadiene)

HMDB0061878
     RDKit          3D
Cyclopentadiene
 11 11  0  0  0  0  0  0  0  0999 V2000
    0.5359    1.1258    0.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7440    0.9130   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9502   -0.5413   -0.1732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3902   -1.1147    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2539   -0.1366    0.2134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0112    2.1109    0.2437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4593    1.7228   -0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6710   -0.9067    0.5950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3322   -0.7348   -1.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6271   -2.1790    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3384   -0.2594    0.3935 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  2  0
  5  1  1  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
M  END
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3D SDF for HMDB0061878 (Cyclopentadiene)

  Mrv1652304272018432D          

  5  5  0  0  0  0            999 V2000
    0.7018    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169    0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2169   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5678   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  4  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0061878

> <DATABASE_NAME>
hmdb

> <SMILES>
C1C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6/c1-2-4-5-3-1/h1-4H,5H2

> <INCHI_KEY>
ZSWFCLXCOIISFI-UHFFFAOYSA-N

> <FORMULA>
C5H6

> <MOLECULAR_WEIGHT>
66.1011

> <EXACT_MASS>
66.046950192

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
11

> <JCHEM_AVERAGE_POLARIZABILITY>
7.68164499385882

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopenta-1,3-diene

> <ALOGPS_LOGP>
1.80

> <JCHEM_LOGP>
1.4990000116666664

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.26166361048897

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
25.2382

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentadiene

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0061878 (Cyclopentadiene)

HMDB0061878
     RDKit          3D
Cyclopentadiene
 11 11  0  0  0  0  0  0  0  0999 V2000
    0.5359    1.1258    0.1318 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7440    0.9130   -0.0921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9502   -0.5413   -0.1732 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3902   -1.1147    0.0359 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2539   -0.1366    0.2134 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0112    2.1109    0.2437 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4593    1.7228   -0.1876 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6710   -0.9067    0.5950 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3322   -0.7348   -1.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6271   -2.1790    0.0422 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3384   -0.2594    0.3935 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  2  0
  5  1  1  0
  1  6  1  0
  2  7  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
M  END
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PDB for HMDB0061878 (Cyclopentadiene)

HEADER    PROTEIN                                 27-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-20         0                                  
HETATM    1  C   UNK     0       1.310   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.405   1.246   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.405  -1.246   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.060   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.060  -0.770   0.000  0.00  0.00           C+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    5                                                       
CONECT    4    2    5                                                       
CONECT    5    3    4                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0061878 (Cyclopentadiene)

COMPND    HMDB0061878
HETATM    1  C1  UNL     1       0.536   1.126   0.132  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.744   0.913  -0.092  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.950  -0.541  -0.173  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.390  -1.115   0.036  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.254  -0.137   0.213  1.00  0.00           C  
HETATM    6  H1  UNL     1       1.011   2.111   0.244  1.00  0.00           H  
HETATM    7  H2  UNL     1      -1.459   1.723  -0.188  1.00  0.00           H  
HETATM    8  H3  UNL     1      -1.671  -0.907   0.595  1.00  0.00           H  
HETATM    9  H4  UNL     1      -1.332  -0.735  -1.203  1.00  0.00           H  
HETATM   10  H5  UNL     1       0.627  -2.179   0.042  1.00  0.00           H  
HETATM   11  H6  UNL     1       2.338  -0.259   0.393  1.00  0.00           H  
CONECT    1    2    2    5    6
CONECT    2    3    7
CONECT    3    4    8    9
CONECT    4    5    5   10
CONECT    5   11
END
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SMILES for HMDB0061878 (Cyclopentadiene)

C1C=CC=C1
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INCHI for HMDB0061878 (Cyclopentadiene)

InChI=1S/C5H6/c1-2-4-5-3-1/h1-4H,5H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1,3-CyclopentadieneChEBI
HCpChEBI
PentoleChEBI
PyropentyleneChEBI
Chemical FormulaC5H6
Average Molecular Weight66.1011
Monoisotopic Molecular Weight66.046950192
IUPAC Namecyclopenta-1,3-diene
Traditional Namecyclopentadiene
CAS Registry Number542-92-7
SMILES
C1C=CC=C1
InChI Identifier
InChI=1S/C5H6/c1-2-4-5-3-1/h1-4H,5H2
InChI KeyZSWFCLXCOIISFI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassOlefins
Direct ParentCycloalkenes
Alternative Parents
Substituents
  • Cycloalkene
  • Unsaturated aliphatic hydrocarbon
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider ID7330
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyclopentadiene
METLIN IDNot Available
PubChem Compound7612
PDB IDNot Available
ChEBI ID30664
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 ReferencesNot Available