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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
Download

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

$$$$
Download

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
Download

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
PropertyValueSource
Water Solubility2.64 g/LALOGPS
logP1.8ALOGPS
logP1.5ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)16.26ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity25.24 m³·mol⁻¹ChemAxon
Polarizability7.68 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+110.87531661259
DarkChem[M-H]-103.93931661259
DeepCCS[M+H]+120.13930932474
DeepCCS[M-H]-117.87430932474
DeepCCS[M-2H]-153.76230932474
DeepCCS[M+Na]+128.28530932474
AllCCS[M+H]+113.732859911
AllCCS[M+H-H2O]+108.332859911
AllCCS[M+NH4]+118.732859911
AllCCS[M+Na]+120.232859911
AllCCS[M-H]-116.632859911
AllCCS[M+Na-2H]-121.132859911
AllCCS[M+HCOO]-126.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.01 minutes32390414
Predicted by Siyang on May 30, 202215.986 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.87 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1651.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid603.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid256.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid490.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid372.0 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid585.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid427.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)285.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1318.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid458.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1089.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid525.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid442.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate575.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA519.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water191.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclopentadieneC1C=CC=C1723.0Standard polar33892256
CyclopentadieneC1C=CC=C1560.8Standard non polar33892256
CyclopentadieneC1C=CC=C1543.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentadiene GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-9000000000-1506fb2a27f3946912d12017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentadiene 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 - Cyclopentadiene 10V, Positive-QTOFsplash10-014i-9000000000-62bdd73b4a908c9405592016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 20V, Positive-QTOFsplash10-014i-9000000000-72326cacd51da43efc0a2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 40V, Positive-QTOFsplash10-0gbc-9000000000-b7f1d718ffc5b55e4b612016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 10V, Negative-QTOFsplash10-014i-9000000000-eb24b03eb6891977faa52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 20V, Negative-QTOFsplash10-014i-9000000000-eb24b03eb6891977faa52016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 40V, Negative-QTOFsplash10-014i-9000000000-babaf67b0f58c3cedcf42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 10V, Positive-QTOFsplash10-014i-9000000000-43e6ea9e2c2f060475ae2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 20V, Positive-QTOFsplash10-014i-9000000000-8bc8385b3d007684b49b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 40V, Positive-QTOFsplash10-014i-9000000000-52789e5d9ca08eeb58b72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 10V, Negative-QTOFsplash10-014i-9000000000-e67cb37c7c41bd3e991d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 20V, Negative-QTOFsplash10-014i-9000000000-e67cb37c7c41bd3e991d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadiene 40V, Negative-QTOFsplash10-014i-9000000000-b4ab4ce534adcb344c9f2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
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