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Showing metabocard for Cyclopentanone (HMDB0031407)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:42:57 UTC
Update Date2023-02-21 17:20:30 UTC
HMDB IDHMDB0031407
Secondary Accession Numbers
  • HMDB31407
Metabolite Identification
Common NameCyclopentanone
DescriptionCyclopentanone belongs to the class of organic compounds known as ketones. These are organic compounds in which a carbonyl group is bonded to two carbon atoms R2C=O (neither R may be a hydrogen atom). Ketones that have one or more alpha-hydrogen atoms undergo keto-enol tautomerization, the tautomer being an enol. Cyclopentanone is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. Thus, cyclopentanone is considered to be an oxygenated hydrocarbon lipid molecule. Cyclopentanone is a cyclic ketone, structurally similar to cyclopentane, consisting of a five-membered ring containing a ketone functional group. Cyclopentanone is a colorless liquid organic compound with a peppermint-like odor. Cyclopentanone is found in various foods, including potato and tomato, and cooked foods, e.g. butter, meats, coffee, roasted peanut. Cyclopentanone is also used as a flavouring ingredient.
Structure
Data?1677000030
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031407 (Cyclopentanone)


  Mrv1652305271900062D          

  6  6  0  0  0  0            999 V2000
   -0.6205    0.2019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2879   -0.2830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0330   -1.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080   -1.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0469   -0.2830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6205    1.0269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1  5  1  0  0  0  0
  1  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0031407 (Cyclopentanone)

HMDB0031407
     RDKit          3D
Cyclopentanone
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.4533   -0.5399    0.3517 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.2599    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6536    1.0901    0.0467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235    0.8385    0.0099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9388   -0.6318    0.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2546   -1.1893   -0.4462 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9205    1.6455    0.9730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9543    1.7015   -0.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2681    0.9860   -0.9958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3752    1.4765    0.7369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8878   -1.0795    0.0166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7526   -0.7974    1.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0342   -1.0084   -1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4612   -2.2320   -0.2005 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  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
Download

3D SDF for HMDB0031407 (Cyclopentanone)


  Mrv1652305271900062D          

  6  6  0  0  0  0            999 V2000
   -0.6205    0.2019    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2879   -0.2830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0330   -1.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2080   -1.0676    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0469   -0.2830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6205    1.0269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  1  5  1  0  0  0  0
  1  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031407

> <DATABASE_NAME>
hmdb

> <SMILES>
O=C1CCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O/c6-5-3-1-2-4-5/h1-4H2

> <INCHI_KEY>
BGTOWKSIORTVQH-UHFFFAOYSA-N

> <FORMULA>
C5H8O

> <MOLECULAR_WEIGHT>
84.1164

> <EXACT_MASS>
84.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.299218774746247

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyclopentanone

> <ALOGPS_LOGP>
0.45

> <JCHEM_LOGP>
1.0436255996666666

> <ALOGPS_LOGS>
-0.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-7.346990119473521

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
23.6464

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.60e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclopentanone

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031407 (Cyclopentanone)

HMDB0031407
     RDKit          3D
Cyclopentanone
 14 14  0  0  0  0  0  0  0  0999 V2000
    2.4533   -0.5399    0.3517 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3142   -0.2599    0.0376 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6536    1.0901    0.0467 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8235    0.8385    0.0099 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9388   -0.6318    0.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2546   -1.1893   -0.4462 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9205    1.6455    0.9730 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9543    1.7015   -0.8025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2681    0.9860   -0.9958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3752    1.4765    0.7369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8878   -1.0795    0.0166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7526   -0.7974    1.4443 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0342   -1.0084   -1.5154 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4612   -2.2320   -0.2005 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  1  0
  5  6  1  0
  6  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  6 13  1  0
  6 14  1  0
M  END
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PDB for HMDB0031407 (Cyclopentanone)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.158   0.377   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.404  -0.528   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.928  -1.993   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.388  -1.993   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.088  -0.528   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.158   1.917   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    1                                                       
CONECT    6    1                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END
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3D PDB for HMDB0031407 (Cyclopentanone)

COMPND    HMDB0031407
HETATM    1  O1  UNL     1       2.453  -0.540   0.352  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.314  -0.260   0.038  1.00  0.00           C  
HETATM    3  C2  UNL     1       0.654   1.090   0.047  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.823   0.839   0.010  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.939  -0.632   0.344  1.00  0.00           C  
HETATM    6  C5  UNL     1       0.255  -1.189  -0.446  1.00  0.00           C  
HETATM    7  H1  UNL     1       0.921   1.645   0.973  1.00  0.00           H  
HETATM    8  H2  UNL     1       0.954   1.702  -0.803  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.268   0.986  -0.996  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.375   1.477   0.737  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.888  -1.079   0.017  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.753  -0.797   1.444  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.034  -1.008  -1.515  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.461  -2.232  -0.201  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    6
CONECT    3    4    7    8
CONECT    4    5    9   10
CONECT    5    6   11   12
CONECT    6   13   14
END
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SMILES for HMDB0031407 (Cyclopentanone)

O=C1CCCC1
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INCHI for HMDB0031407 (Cyclopentanone)

InChI=1S/C5H8O/c6-5-3-1-2-4-5/h1-4H2
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
KetocyclopentaneChEBI
KetopentamethyleneChEBI
OxocyclopentaneChEBI
3-Acetyl-6-methyl-pyran-2,4(3H)-dioneHMDB
Adipic ketoneHMDB
AdipinketonHMDB
CPHMDB
DumasinHMDB
DumasineHMDB
FEMA 3910HMDB
Chemical FormulaC5H8O
Average Molecular Weight84.1164
Monoisotopic Molecular Weight84.057514878
IUPAC Namecyclopentanone
Traditional Namecyclopentanone
CAS Registry Number120-92-3
SMILES
O=C1CCCC1
InChI Identifier
InChI=1S/C5H8O/c6-5-3-1-2-4-5/h1-4H2
InChI KeyBGTOWKSIORTVQH-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 Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-58 °CNot Available
Boiling Point130.00 to 131.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility60810 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.38Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility66 g/LALOGPS
logP0.45ALOGPS
logP1.04ChemAxon
logS-0.11ALOGPS
pKa (Strongest Basic)-7.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity23.65 m³·mol⁻¹ChemAxon
Polarizability9.3 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]+115.42331661259
DarkChem[M-H]-109.32731661259
DeepCCS[M+H]+124.86630932474
DeepCCS[M-H]-122.87730932474
DeepCCS[M-2H]-158.27130932474
DeepCCS[M+Na]+132.72330932474
AllCCS[M+H]+119.332859911
AllCCS[M+H-H2O]+114.332859911
AllCCS[M+NH4]+124.032859911
AllCCS[M+Na]+125.432859911
AllCCS[M-H]-119.232859911
AllCCS[M+Na-2H]-123.132859911
AllCCS[M+HCOO]-127.332859911

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, 2022.2.43 minutes32390414
Predicted by Siyang on May 30, 202211.6294 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.11 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1450.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid442.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid157.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid298.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid260.9 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid380.5 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 Acid475.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)151.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid975.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid293.0 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid945.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid267.3 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid328.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate550.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA405.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water146.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
CyclopentanoneO=C1CCCC11132.6Standard polar33892256
CyclopentanoneO=C1CCCC1727.6Standard non polar33892256
CyclopentanoneO=C1CCCC1773.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cyclopentanone,1TMS,isomer #1C[Si](C)(C)OC1=CCCC1994.2Semi standard non polar33892256
Cyclopentanone,1TMS,isomer #1C[Si](C)(C)OC1=CCCC11012.9Standard non polar33892256
Cyclopentanone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CCCC11220.5Semi standard non polar33892256
Cyclopentanone,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1=CCCC11190.4Standard 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 IDFDB003481
KNApSAcK IDC00010807
Chemspider ID8141
KEGG Compound IDC00557
BioCyc IDCYCLOPENTANONE
BiGG IDNot Available
Wikipedia LinkCyclopentanone
METLIN IDNot Available
PubChem Compound8452
PDB IDMFW
ChEBI ID16486
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1017921
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .