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Showing metabocard for 2-Cyclopenten-1-one (HMDB0245092)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 22:11:50 UTC
Update Date2021-09-26 22:53:19 UTC
HMDB IDHMDB0245092
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Cyclopenten-1-one
Description2-Cyclopenten-1-one, also known as cyclopent-2-enone, belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety. Based on a literature review a significant number of articles have been published on 2-Cyclopenten-1-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 2-cyclopenten-1-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 2-Cyclopenten-1-one 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 HMDB0245092 (2-Cyclopenten-1-one)


  Mrv1533004161513122D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
M  END
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3D MOL for HMDB0245092 (2-Cyclopenten-1-one)

HMDB0245092
     RDKit          3D
2-Cyclopenten-1-one
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.7254    2.3689    0.2584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2804    1.2404    0.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0513    0.7646    0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0725   -0.5563    0.3821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2634   -1.0588    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9522    0.0956   -0.6035 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8937    1.4501    0.5416 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9921   -1.1242    0.6069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7766   -1.3111    1.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2635   -1.9601   -0.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0477    0.0890   -0.4373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7004    0.0018   -1.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  4  8  1  0
  5  9  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0245092 (2-Cyclopenten-1-one)


  Mrv1533004161513122D          

  6  6  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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  1  0  0  0  0
  5  6  2  0  0  0  0
  2  6  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0245092

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O/c6-5-3-1-2-4-5/h1,3H,2,4H2

> <INCHI_KEY>
BZKFMUIJRXWWQK-UHFFFAOYSA-N

> <FORMULA>
C5H6O

> <MOLECULAR_WEIGHT>
82.102

> <EXACT_MASS>
82.041864813

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.536679233666966

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopent-2-en-1-one

> <ALOGPS_LOGP>
0.46

> <JCHEM_LOGP>
1.0414490893333332

> <ALOGPS_LOGS>
-0.04

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.98978131613268

> <JCHEM_PKA_STRONGEST_BASIC>
-4.7073230547290965

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
24.739699999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.50e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentenone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0245092 (2-Cyclopenten-1-one)

HMDB0245092
     RDKit          3D
2-Cyclopenten-1-one
 12 12  0  0  0  0  0  0  0  0999 V2000
   -0.7254    2.3689    0.2584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2804    1.2404    0.0334 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0513    0.7646    0.3547 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0725   -0.5563    0.3821 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2634   -1.0588    0.0779 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9522    0.0956   -0.6035 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8937    1.4501    0.5416 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9921   -1.1242    0.6069 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7766   -1.3111    1.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2635   -1.9601   -0.5697 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0477    0.0890   -0.4373 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7004    0.0018   -1.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  4  8  1  0
  5  9  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
M  END
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PDB for HMDB0245092 (2-Cyclopenten-1-one)

HEADER    PROTEIN                                 16-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-APR-15         0                                  
HETATM    1  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0245092 (2-Cyclopenten-1-one)

COMPND    HMDB0245092
HETATM    1  O1  UNL     1      -0.725   2.369   0.258  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.280   1.240   0.033  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.051   0.765   0.355  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.073  -0.556   0.382  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.263  -1.059   0.078  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.952   0.096  -0.603  1.00  0.00           C  
HETATM    7  H1  UNL     1       1.894   1.450   0.542  1.00  0.00           H  
HETATM    8  H2  UNL     1       1.992  -1.124   0.607  1.00  0.00           H  
HETATM    9  H3  UNL     1      -0.777  -1.311   1.054  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.263  -1.960  -0.570  1.00  0.00           H  
HETATM   11  H5  UNL     1      -2.048   0.089  -0.437  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.700   0.002  -1.699  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    4    7
CONECT    4    5    8
CONECT    5    6    9   10
CONECT    6   11   12
END
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SMILES for HMDB0245092 (2-Cyclopenten-1-one)

O=C1CCC=C1
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INCHI for HMDB0245092 (2-Cyclopenten-1-one)

InChI=1S/C5H6O/c6-5-3-1-2-4-5/h1,3H,2,4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-CyclopentenoneChEBI
Cyclopent-2-enoneChEBI
Cyclopenten-3-oneChEBI
CyclopentenoneChEBI
Chemical FormulaC5H6O
Average Molecular Weight82.102
Monoisotopic Molecular Weight82.041864813
IUPAC Namecyclopent-2-en-1-one
Traditional Namecyclopentenone
CAS Registry NumberNot Available
SMILES
O=C1CCC=C1
InChI Identifier
InChI=1S/C5H6O/c6-5-3-1-2-4-5/h1,3H,2,4H2
InChI KeyBZKFMUIJRXWWQK-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentCyclic ketones
Alternative Parents
Substituents
  • Cyclic ketone
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP0.46ALOGPS
logP1.04ChemAxon
logS-0.04ALOGPS
pKa (Strongest Acidic)16.99ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity24.74 m³·mol⁻¹ChemAxon
Polarizability8.54 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]+120.07330932474
DeepCCS[M-H]-118.03630932474
DeepCCS[M-2H]-153.70730932474
DeepCCS[M+Na]+128.33830932474
AllCCS[M+H]+118.332859911
AllCCS[M+H-H2O]+113.232859911
AllCCS[M+NH4]+123.132859911
AllCCS[M+Na]+124.532859911
AllCCS[M-H]-117.532859911
AllCCS[M+Na-2H]-121.332859911
AllCCS[M+HCOO]-125.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Cyclopenten-1-oneO=C1CCC=C11336.5Standard polar33892256
2-Cyclopenten-1-oneO=C1CCC=C1773.9Standard non polar33892256
2-Cyclopenten-1-oneO=C1CCC=C1822.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Cyclopenten-1-one,1TMS,isomer #1C[Si](C)(C)OC1=CCC=C11066.4Semi standard non polar33892256
2-Cyclopenten-1-one,1TMS,isomer #1C[Si](C)(C)OC1=CCC=C1964.0Standard non polar33892256
2-Cyclopenten-1-one,1TMS,isomer #1C[Si](C)(C)OC1=CCC=C11150.1Standard polar33892256
2-Cyclopenten-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CCC=C11310.7Semi standard non polar33892256
2-Cyclopenten-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CCC=C11150.9Standard non polar33892256
2-Cyclopenten-1-one,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CCC=C11347.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Cyclopenten-1-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-0f89-9000000000-bcfd5866f8569847ef682021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Cyclopenten-1-one 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 - 2-Cyclopenten-1-one 10V, Positive-QTOFsplash10-001i-9000000000-91ebef4449219553f3f12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Cyclopenten-1-one 20V, Positive-QTOFsplash10-053u-9000000000-d394c69c979fddc8b0ae2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Cyclopenten-1-one 40V, Positive-QTOFsplash10-0006-9000000000-205ac41037e7c85fb2322021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Cyclopenten-1-one 10V, Negative-QTOFsplash10-001i-9000000000-e75a5149c7c9bbbbc6e12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Cyclopenten-1-one 20V, Negative-QTOFsplash10-001i-9000000000-e75a5149c7c9bbbbc6e12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Cyclopenten-1-one 40V, Negative-QTOFsplash10-0zgi-9000000000-974ba5057d5209a8b3672021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-12Wishart 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 IDC00001313
Chemspider ID12999
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkCyclopentenone
METLIN IDNot Available
PubChem Compound13588
PDB IDNot Available
ChEBI ID141550
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1174961
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 ]