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Showing metabocard for 4-Penten-2-one (HMDB0031606)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:44:19 UTC
Update Date2023-02-21 17:20:58 UTC
HMDB IDHMDB0031606
Secondary Accession Numbers
  • HMDB31606
Metabolite Identification
Common Name4-Penten-2-one
Description4-Penten-2-one 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. Thus, 4-penten-2-one is considered to be an oxygenated hydrocarbon. 4-Penten-2-one has been detected, but not quantified in, fruits and tamarinds (Tamarindus indica). This could make 4-penten-2-one a potential biomarker for the consumption of these foods. 4-Penten-2-one is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on 4-Penten-2-one.
Structure
Data?1677000058
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031606 (4-Penten-2-one)


  Mrv0541 05061306012D          

  6  5  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  2  0  0  0  0
M  END
Download

3D MOL for HMDB0031606 (4-Penten-2-one)

HMDB0031606
     RDKit          3D
4-Penten-2-one
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.3517    0.2650    0.2352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1423    0.4558   -0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2427   -0.6807   -0.5565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0032   -0.6320    0.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0110    0.4321    0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2167   -1.4838    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0195    1.0885    0.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7608   -0.7368    0.4190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7880    1.4691   -0.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0524   -0.7407   -1.6214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7607   -1.6582   -0.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9179    0.9207   -0.9202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8110    1.1946    0.8618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0533    0.1063    0.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  5 12  1  0
  5 13  1  0
  5 14  1  0
M  END
Download

3D SDF for HMDB0031606 (4-Penten-2-one)


  Mrv0541 05061306012D          

  6  5  0  0  0  0            999 V2000
    1.2375    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  3  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031606

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=O)CC=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O/c1-3-4-5(2)6/h3H,1,4H2,2H3

> <INCHI_KEY>
PNJWIWWMYCMZRO-UHFFFAOYSA-N

> <FORMULA>
C5H8O

> <MOLECULAR_WEIGHT>
84.1164

> <EXACT_MASS>
84.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
9.494209362282714

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pent-4-en-2-one

> <ALOGPS_LOGP>
0.66

> <JCHEM_LOGP>
0.9473963339999997

> <ALOGPS_LOGS>
-0.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.88525840835349

> <JCHEM_PKA_STRONGEST_BASIC>
-7.35951587867593

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
25.4668

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pent-4-en-2-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0031606 (4-Penten-2-one)

HMDB0031606
     RDKit          3D
4-Penten-2-one
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.3517    0.2650    0.2352 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1423    0.4558   -0.2329 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2427   -0.6807   -0.5565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0032   -0.6320    0.2522 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0110    0.4321    0.0580 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2167   -1.4838    1.1091 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0195    1.0885    0.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7608   -0.7368    0.4190 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7880    1.4691   -0.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0524   -0.7407   -1.6214 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7607   -1.6582   -0.3526 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9179    0.9207   -0.9202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8110    1.1946    0.8618 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0533    0.1063    0.1716 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  4  6  2  0
  1  7  1  0
  1  8  1  0
  2  9  1  0
  3 10  1  0
  3 11  1  0
  5 12  1  0
  5 13  1  0
  5 14  1  0
M  END
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PDB for HMDB0031606 (4-Penten-2-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       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    5                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    2    4    6                                                  
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0031606 (4-Penten-2-one)

COMPND    HMDB0031606
HETATM    1  C1  UNL     1       2.352   0.265   0.235  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.142   0.456  -0.233  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.243  -0.681  -0.556  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.003  -0.632   0.252  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.011   0.432   0.058  1.00  0.00           C  
HETATM    6  O1  UNL     1      -1.217  -1.484   1.109  1.00  0.00           O  
HETATM    7  H1  UNL     1       3.019   1.089   0.474  1.00  0.00           H  
HETATM    8  H2  UNL     1       2.761  -0.737   0.419  1.00  0.00           H  
HETATM    9  H3  UNL     1       0.788   1.469  -0.387  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.052  -0.741  -1.621  1.00  0.00           H  
HETATM   11  H5  UNL     1       0.761  -1.658  -0.353  1.00  0.00           H  
HETATM   12  H6  UNL     1      -1.918   0.921  -0.920  1.00  0.00           H  
HETATM   13  H7  UNL     1      -1.811   1.195   0.862  1.00  0.00           H  
HETATM   14  H8  UNL     1      -3.053   0.106   0.172  1.00  0.00           H  
CONECT    1    2    2    7    8
CONECT    2    3    9
CONECT    3    4   10   11
CONECT    4    5    6    6
CONECT    5   12   13   14
END
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SMILES for HMDB0031606 (4-Penten-2-one)

CC(=O)CC=C
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INCHI for HMDB0031606 (4-Penten-2-one)

InChI=1S/C5H8O/c1-3-4-5(2)6/h3H,1,4H2,2H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Allyl methyl ketoneHMDB
VinylacetoneHMDB
Chemical FormulaC5H8O
Average Molecular Weight84.1164
Monoisotopic Molecular Weight84.057514878
IUPAC Namepent-4-en-2-one
Traditional Namepent-4-en-2-one
CAS Registry Number13891-87-7
SMILES
CC(=O)CC=C
InChI Identifier
InChI=1S/C5H8O/c1-3-4-5(2)6/h3H,1,4H2,2H3
InChI KeyPNJWIWWMYCMZRO-UHFFFAOYSA-N
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentKetones
Alternative Parents
Substituents
  • Ketone
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
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 Point93.00 to 94.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility38630 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP0.734 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility22.6 g/LALOGPS
logP0.66ALOGPS
logP0.95ChemAxon
logS-0.57ALOGPS
pKa (Strongest Acidic)16.89ChemAxon
pKa (Strongest Basic)-7.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity25.47 m³·mol⁻¹ChemAxon
Polarizability9.49 ųChemAxon
Number of Rings0ChemAxon
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]+116.40231661259
DarkChem[M-H]-110.1531661259
DeepCCS[M+H]+122.64130932474
DeepCCS[M-H]-120.63930932474
DeepCCS[M-2H]-156.08130932474
DeepCCS[M+Na]+130.61230932474
AllCCS[M+H]+121.132859911
AllCCS[M+H-H2O]+116.632859911
AllCCS[M+NH4]+125.432859911
AllCCS[M+Na]+126.632859911
AllCCS[M-H]-126.832859911
AllCCS[M+Na-2H]-131.432859911
AllCCS[M+HCOO]-136.432859911

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, 2022.2.75 minutes32390414
Predicted by Siyang on May 30, 202211.4348 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.34 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid57.4 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1469.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid428.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid159.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid297.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid125.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid378.2 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 Acid476.2 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)129.2 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid913.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid308.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid988.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid311.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid304.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate492.8 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA394.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water77.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
4-Penten-2-oneCC(=O)CC=C1000.7Standard polar33892256
4-Penten-2-oneCC(=O)CC=C654.1Standard non polar33892256
4-Penten-2-oneCC(=O)CC=C662.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
4-Penten-2-one,1TMS,isomer #1C=CC=C(C)O[Si](C)(C)C937.0Semi standard non polar33892256
4-Penten-2-one,1TMS,isomer #1C=CC=C(C)O[Si](C)(C)C871.1Standard non polar33892256
4-Penten-2-one,1TMS,isomer #2C=CCC(=C)O[Si](C)(C)C846.0Semi standard non polar33892256
4-Penten-2-one,1TMS,isomer #2C=CCC(=C)O[Si](C)(C)C877.7Standard non polar33892256
4-Penten-2-one,1TBDMS,isomer #1C=CC=C(C)O[Si](C)(C)C(C)(C)C1154.7Semi standard non polar33892256
4-Penten-2-one,1TBDMS,isomer #1C=CC=C(C)O[Si](C)(C)C(C)(C)C1083.9Standard non polar33892256
4-Penten-2-one,1TBDMS,isomer #2C=CCC(=C)O[Si](C)(C)C(C)(C)C1072.4Semi standard non polar33892256
4-Penten-2-one,1TBDMS,isomer #2C=CCC(=C)O[Si](C)(C)C(C)(C)C1087.4Standard 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 IDFDB008242
KNApSAcK IDC00054486
Chemspider ID75618
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound83797
PDB IDNot Available
ChEBI ID87508
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1458821
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .