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Showing metabocard for 2-Methyl-2-cyclopenten-1-one (HMDB0031545)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:43:58 UTC
Update Date2023-02-21 17:20:47 UTC
HMDB IDHMDB0031545
Secondary Accession Numbers
  • HMDB31545
Metabolite Identification
Common Name2-Methyl-2-cyclopenten-1-one
Description2-Methyl-2-cyclopenten-1-one, also known as aaee-ethanol or N-acryloylaminoethoxyethanol, 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 small amount of articles have been published on 2-Methyl-2-cyclopenten-1-one.
Structure
Data?1677000047
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)


  Mrv0541 05061305592D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    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
    1.2352    0.6294    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
    0.5678    1.1143    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
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

HMDB0031545
     RDKit          3D
2-Methyl-2-cyclopenten-1-one
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1778    0.0924   -0.1372 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6976   -0.0018   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0092   -1.0999    0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4550   -0.8120    0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5033    0.6746    0.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2215    1.1192   -0.3257 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0217    2.2091   -0.8993 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093   -0.9243   -0.2344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273    0.5870    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4852    0.6706   -1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4523   -2.0587    0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0290   -1.3496    0.8616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9126   -1.1035   -0.9013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4693    0.8288    1.4020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3713    1.1682   -0.1680 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  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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3D SDF for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)


  Mrv0541 05061305592D          

  7  7  0  0  0  0            999 V2000
    0.5678    1.9393    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
    1.2352    0.6294    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
    0.5678    1.1143    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
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  2  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031545

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=CCCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H8O/c1-5-3-2-4-6(5)7/h3H,2,4H2,1H3

> <INCHI_KEY>
ZSBWUNDRDHVNJL-UHFFFAOYSA-N

> <FORMULA>
C6H8O

> <MOLECULAR_WEIGHT>
96.1271

> <EXACT_MASS>
96.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
10.60437889474002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
1.4369995786666665

> <ALOGPS_LOGS>
-0.48

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.6493410965378

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
29.0968

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-cyclopenten-1-one, 2-methyl-

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

HMDB0031545
     RDKit          3D
2-Methyl-2-cyclopenten-1-one
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.1778    0.0924   -0.1372 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6976   -0.0018   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0092   -1.0999    0.1159 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4550   -0.8120    0.0676 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5033    0.6746    0.2855 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2215    1.1192   -0.3257 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0217    2.2091   -0.8993 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6093   -0.9243   -0.2344 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273    0.5870    0.7751 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4852    0.6706   -1.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4523   -2.0587    0.3049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0290   -1.3496    0.8616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9126   -1.1035   -0.9013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4693    0.8288    1.4020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3713    1.1682   -0.1680 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  1  0
  5  6  1  0
  6  7  2  0
  6  2  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
M  END
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PDB for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.830  -0.290   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       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   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
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    1    3    6                                                  
CONECT    6    4    5    7                                                  
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   14    0
END
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3D PDB for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

COMPND    HMDB0031545
HETATM    1  C1  UNL     1       2.178   0.092  -0.137  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.698  -0.002  -0.109  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.009  -1.100   0.116  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.455  -0.812   0.068  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.503   0.675   0.286  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.221   1.119  -0.326  1.00  0.00           C  
HETATM    7  O1  UNL     1       0.022   2.209  -0.899  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.609  -0.924  -0.234  1.00  0.00           H  
HETATM    9  H2  UNL     1       2.527   0.587   0.775  1.00  0.00           H  
HETATM   10  H3  UNL     1       2.485   0.671  -1.038  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.452  -2.059   0.305  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.029  -1.350   0.862  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.913  -1.104  -0.901  1.00  0.00           H  
HETATM   14  H7  UNL     1      -1.469   0.829   1.402  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.371   1.168  -0.168  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3    6
CONECT    3    4   11
CONECT    4    5   12   13
CONECT    5    6   14   15
CONECT    6    7    7
END
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SMILES for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

CC1=CCCC1=O
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INCHI for HMDB0031545 (2-Methyl-2-cyclopenten-1-one)

InChI=1S/C6H8O/c1-5-3-2-4-6(5)7/h3H,2,4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Methyl-2-cycloheptenoneHMDB
2-Methyl-2-cyclopentenoneHMDB
2-Methylcyclopent-2-en-1-oneHMDB
Aaee-ethanolHMDB
Methyl-cyclopentenoneHMDB
N-(2-(2-Hydroxyethoxy)ethyl)-2-propenamideHMDB
N-AcryloylaminoethoxyethanolHMDB
Chemical FormulaC6H8O
Average Molecular Weight96.1271
Monoisotopic Molecular Weight96.057514878
IUPAC Name2-methylcyclopent-2-en-1-one
Traditional Name2-cyclopenten-1-one, 2-methyl-
CAS Registry Number1120-73-6
SMILES
CC1=CCCC1=O
InChI Identifier
InChI=1S/C6H8O/c1-5-3-2-4-6(5)7/h3H,2,4H2,1H3
InChI KeyZSBWUNDRDHVNJL-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 locationRoute of exposureSource
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 Solubility32 g/LALOGPS
logP0.84ALOGPS
logP1.44ChemAxon
logS-0.48ALOGPS
pKa (Strongest Basic)-4.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity29.1 m³·mol⁻¹ChemAxon
Polarizability10.6 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]+119.60931661259
DarkChem[M-H]-114.2731661259
DeepCCS[M+H]+126.29130932474
DeepCCS[M-H]-123.93630932474
DeepCCS[M-2H]-160.11630932474
DeepCCS[M+Na]+134.53430932474
AllCCS[M+H]+119.032859911
AllCCS[M+H-H2O]+114.032859911
AllCCS[M+NH4]+123.732859911
AllCCS[M+Na]+125.132859911
AllCCS[M-H]-118.832859911
AllCCS[M+Na-2H]-121.932859911
AllCCS[M+HCOO]-125.432859911

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, 2022.3.29 minutes32390414
Predicted by Siyang on May 30, 202210.6801 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.63 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1529.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid390.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid143.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid257.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid88.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid323.2 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 Acid411.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)99.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid858.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid297.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid858.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid278.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid309.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate486.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA364.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water92.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methyl-2-cyclopenten-1-oneCC1=CCCC1=O1322.0Standard polar33892256
2-Methyl-2-cyclopenten-1-oneCC1=CCCC1=O856.7Standard non polar33892256
2-Methyl-2-cyclopenten-1-oneCC1=CCCC1=O898.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Methyl-2-cyclopenten-1-one,1TMS,isomer #1CC1=CCC=C1O[Si](C)(C)C1082.5Semi standard non polar33892256
2-Methyl-2-cyclopenten-1-one,1TMS,isomer #1CC1=CCC=C1O[Si](C)(C)C1085.1Standard non polar33892256
2-Methyl-2-cyclopenten-1-one,1TBDMS,isomer #1CC1=CCC=C1O[Si](C)(C)C(C)(C)C1309.2Semi standard non polar33892256
2-Methyl-2-cyclopenten-1-one,1TBDMS,isomer #1CC1=CCC=C1O[Si](C)(C)C(C)(C)C1251.7Standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB008155
KNApSAcK IDNot Available
Chemspider ID13628
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound14266
PDB IDNot Available
ChEBI IDNot Available
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. Bol R, Poirier N, Balesdent J, Gleixner G: Molecular turnover time of soil organic matter in particle-size fractions of an arable soil. Rapid Commun Mass Spectrom. 2009 Aug 30;23(16):2551-8. doi: 10.1002/rcm.4124. [PubMed:19603490 ]
  2. Mandal M, Yun H, Dudley GB, Lin S, Tan DS, Danishefsky SJ: Total synthesis of guanacastepene a: a route to enantiomeric control. J Org Chem. 2005 Dec 23;70(26):10619-37. [PubMed:16355979 ]
  3. Dudley GB, Danishefsky SJ: A four-step synthesis of the hydroazulene core of guanacastepene. Org Lett. 2001 Jul 26;3(15):2399-402. [PubMed:11463326 ]
  4. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .