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Showing metabocard for Cyclopentadienyl (HMDB0250665)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:45:39 UTC
Update Date2021-09-26 23:02:16 UTC
HMDB IDHMDB0250665
Secondary Accession NumbersNone
Metabolite Identification
Common NameCyclopentadienyl
Descriptioncyclopentadienyl belongs to the class of organic compounds known as cycloalkenes. These are unsaturated monocyclic hydrocarbons having one endocyclic double bond. Based on a literature review a significant number of articles have been published on cyclopentadienyl. This compound has been identified in human blood as reported by (PMID: 31557052 ). Cyclopentadienyl is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Cyclopentadienyl 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 HMDB0250665 (Cyclopentadienyl)


  Mrv1652309112109452D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    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  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
M  RAD  1   3   2
M  END
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3D MOL for HMDB0250665 (Cyclopentadienyl)

HMDB0250665
     RDKit          3D
Cyclopentadienyl
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.2279    0.1320   -0.1112 C   0  0  0  0  0  3  0  0  0  0  0  0
   -0.2197    1.2147   -0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635    0.6329   -0.0835 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7953   -0.8139   -0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721   -1.1406   -0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9135    0.1914    0.7654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4676    2.2670   -0.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9114    1.1701   -0.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5916   -1.5507   -0.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9610   -2.1029   -0.0701 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  4  9  1  0
  5 10  1  0
M  RAD  1   1   2
M  END
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3D SDF for HMDB0250665 (Cyclopentadienyl)


  Mrv1652309112109452D          

  5  5  0  0  0  0            999 V2000
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    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  1  0  0  0  0
  4  5  2  0  0  0  0
  1  5  1  0  0  0  0
M  RAD  1   3   2
M  END
> <DATABASE_ID>
HMDB0250665

> <DATABASE_NAME>
hmdb

> <SMILES>
[CH]1C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5/c1-2-4-5-3-1/h1-5H

> <INCHI_KEY>
HPYIUKIBUJFXII-UHFFFAOYSA-N

> <FORMULA>
C5H5

> <MOLECULAR_WEIGHT>
65.095

> <EXACT_MASS>
65.039125161

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
7.335561561112689

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopenta-2,4-dien-1-yl

> <ALOGPS_LOGP>
1.80

> <JCHEM_LOGP>
1.3991

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
24.031100000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentadienyl

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0250665 (Cyclopentadienyl)

HMDB0250665
     RDKit          3D
Cyclopentadienyl
 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.2279    0.1320   -0.1112 C   0  0  0  0  0  3  0  0  0  0  0  0
   -0.2197    1.2147   -0.1124 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9635    0.6329   -0.0835 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7953   -0.8139   -0.0625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4721   -1.1406   -0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9135    0.1914    0.7654 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4676    2.2670   -0.1338 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9114    1.1701   -0.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5916   -1.5507   -0.0373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9610   -2.1029   -0.0701 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  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
  4  9  1  0
  5 10  1  0
M  RAD  1   1   2
M  END
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PDB for HMDB0250665 (Cyclopentadienyl)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
CONECT    1    2    5                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
MASTER        0    0    0    0    0    0    0    0    5    0   10    0
END
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3D PDB for HMDB0250665 (Cyclopentadienyl)

COMPND    HMDB0250665
HETATM    1  C1  UNL     1      -1.228   0.132  -0.111  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.220   1.215  -0.112  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.964   0.633  -0.083  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.795  -0.814  -0.062  1.00  0.00           C  
HETATM    5  C5  UNL     1      -0.472  -1.141  -0.078  1.00  0.00           C  
HETATM    6  H1  UNL     1      -1.913   0.191   0.765  1.00  0.00           H  
HETATM    7  H2  UNL     1      -0.468   2.267  -0.134  1.00  0.00           H  
HETATM    8  H3  UNL     1       1.911   1.170  -0.077  1.00  0.00           H  
HETATM    9  H4  UNL     1       1.592  -1.551  -0.037  1.00  0.00           H  
HETATM   10  H5  UNL     1      -0.961  -2.103  -0.070  1.00  0.00           H  
CONECT    1    2    5    6
CONECT    2    3    3    7
CONECT    3    4    8
CONECT    4    5    5    9
CONECT    5   10
END
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SMILES for HMDB0250665 (Cyclopentadienyl)

[CH]1C=CC=C1
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INCHI for HMDB0250665 (Cyclopentadienyl)

InChI=1S/C5H5/c1-2-4-5-3-1/h1-5H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Cyclopentadienyl radicalChEBI
Chemical FormulaC5H5
Average Molecular Weight65.095
Monoisotopic Molecular Weight65.039125161
IUPAC Namecyclopenta-2,4-dien-1-yl
Traditional Namecyclopentadienyl
CAS Registry NumberNot Available
SMILES
[CH]1C=CC=C1
InChI Identifier
InChI=1S/C5H5/c1-2-4-5-3-1/h1-5H
InChI KeyHPYIUKIBUJFXII-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
Not AvailableNot 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
logP1.8ALOGPS
logP1.4ChemAxon
logS-1.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.03 m³·mol⁻¹ChemAxon
Polarizability7.34 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
DeepCCS[M+H]+114.65730932474
DeepCCS[M-H]-112.48730932474
DeepCCS[M-2H]-148.31430932474
DeepCCS[M+Na]+123.03330932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Cyclopentadienyl[CH]1C=CC=C1708.7Standard polar33892256
Cyclopentadienyl[CH]1C=CC=C1524.7Standard non polar33892256
Cyclopentadienyl[CH]1C=CC=C1506.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentadienyl GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-9000000000-3b6699603012e18a2a802021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cyclopentadienyl 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 - Cyclopentadienyl 10V, Negative-QTOFsplash10-03di-9000000000-f889ac571dd693fac9852021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadienyl 20V, Negative-QTOFsplash10-03di-9000000000-cf5bb1b760390c473c092021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadienyl 40V, Negative-QTOFsplash10-03di-9000000000-f8d0d9e923ebf2d70b0d2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadienyl 10V, Positive-QTOFsplash10-014i-9000000000-fd2f07e6114ed5a619f92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadienyl 20V, Positive-QTOFsplash10-014r-9000000000-e9ae5a025b4a5f5fd2fa2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cyclopentadienyl 40V, Positive-QTOFsplash10-014r-9000000000-87877e6e656ac960ffc62021-10-12Wishart 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 ID121110
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyclopentadienyl
METLIN IDNot Available
PubChem Compound137443
PDB IDNot Available
ChEBI ID36769
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 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 ]