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Showing metabocard for 1,4-Pentadien-3-one (HMDB0244222)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 21:23:53 UTC
Update Date2021-09-26 22:51:50 UTC
HMDB IDHMDB0244222
Secondary Accession NumbersNone
Metabolite Identification
Common Name1,4-Pentadien-3-one
Description1,4-Pentadien-3-one belongs to the class of organic compounds known as enones. Enones are compounds containing the enone functional group, with the structure RC(=O)CR'. Based on a literature review a significant number of articles have been published on 1,4-Pentadien-3-one. This compound has been identified in human blood as reported by (PMID: 31557052 ). 1,4-pentadien-3-one is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 1,4-Pentadien-3-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 HMDB0244222 (1,4-Pentadien-3-one)


  Mrv1652309102123242D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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 O   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 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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0244222 (1,4-Pentadien-3-one)

HMDB0244222
     RDKit          3D
1,4-Pentadien-3-one
 12 11  0  0  0  0  0  0  0  0999 V2000
   -2.3750    0.4398    0.3433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3267   -0.2435   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0183    0.1890    0.2391 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1834    1.2403    0.8974 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2168   -0.5209   -0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4337   -0.1069    0.1073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3829    0.1278    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2552    1.3534    0.9148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4831   -1.1440   -0.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0828   -1.4481   -0.7573 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2778   -0.6785   -0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6101    0.7917    0.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  3
  1  7  1  0
  1  8  1  0
  2  9  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
M  END
Download

3D SDF for HMDB0244222 (1,4-Pentadien-3-one)


  Mrv1652309102123242D          

  6  5  0  0  0  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    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 O   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 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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0244222

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O/c1-3-5(6)4-2/h3-4H,1-2H2

> <INCHI_KEY>
UCUUFSAXZMGPGH-UHFFFAOYSA-N

> <FORMULA>
C5H6O

> <MOLECULAR_WEIGHT>
82.102

> <EXACT_MASS>
82.041864813

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.744347657648188

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
penta-1,4-dien-3-one

> <ALOGPS_LOGP>
0.83

> <JCHEM_LOGP>
1.618865822333333

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.424037335877699

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
25.490199999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
penta-1,4-dien-3-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0244222 (1,4-Pentadien-3-one)

HMDB0244222
     RDKit          3D
1,4-Pentadien-3-one
 12 11  0  0  0  0  0  0  0  0999 V2000
   -2.3750    0.4398    0.3433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3267   -0.2435   -0.0595 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0183    0.1890    0.2391 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1834    1.2403    0.8974 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2168   -0.5209   -0.1769 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4337   -0.1069    0.1073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3829    0.1278    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2552    1.3534    0.9148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4831   -1.1440   -0.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0828   -1.4481   -0.7573 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2778   -0.6785   -0.2303 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6101    0.7917    0.6708 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  3
  1  7  1  0
  1  8  1  0
  2  9  1  0
  5 10  1  0
  6 11  1  0
  6 12  1  0
M  END
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PDB for HMDB0244222 (1,4-Pentadien-3-one)

HEADER    PROTEIN                                 10-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-21         0                                  
HETATM    1  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    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 HMDB0244222 (1,4-Pentadien-3-one)

COMPND    HMDB0244222
HETATM    1  C1  UNL     1      -2.375   0.440   0.343  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.327  -0.244  -0.059  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.018   0.189   0.239  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.183   1.240   0.897  1.00  0.00           O  
HETATM    5  C4  UNL     1       1.217  -0.521  -0.177  1.00  0.00           C  
HETATM    6  C5  UNL     1       2.434  -0.107   0.107  1.00  0.00           C  
HETATM    7  H1  UNL     1      -3.383   0.128   0.127  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.255   1.353   0.915  1.00  0.00           H  
HETATM    9  H3  UNL     1      -1.483  -1.144  -0.624  1.00  0.00           H  
HETATM   10  H4  UNL     1       1.083  -1.448  -0.757  1.00  0.00           H  
HETATM   11  H5  UNL     1       3.278  -0.679  -0.230  1.00  0.00           H  
HETATM   12  H6  UNL     1       2.610   0.792   0.671  1.00  0.00           H  
CONECT    1    2    2    7    8
CONECT    2    3    9
CONECT    3    4    4    5
CONECT    5    6    6   10
CONECT    6   11   12
END
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SMILES for HMDB0244222 (1,4-Pentadien-3-one)

C=CC(=O)C=C
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INCHI for HMDB0244222 (1,4-Pentadien-3-one)

InChI=1S/C5H6O/c1-3-5(6)4-2/h3-4H,1-2H2
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H6O
Average Molecular Weight82.102
Monoisotopic Molecular Weight82.041864813
IUPAC Namepenta-1,4-dien-3-one
Traditional Namepenta-1,4-dien-3-one
CAS Registry NumberNot Available
SMILES
C=CC(=O)C=C
InChI Identifier
InChI=1S/C5H6O/c1-3-5(6)4-2/h3-4H,1-2H2
InChI KeyUCUUFSAXZMGPGH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as enones. Enones are compounds containing the enone functional group, with the structure RC(=O)CR'.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentEnones
Alternative Parents
Substituents
  • Enone
  • Acryloyl-group
  • Ketone
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
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
logP0.83ALOGPS
logP1.62ChemAxon
logS-1.3ALOGPS
pKa (Strongest Basic)-4.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity25.49 m³·mol⁻¹ChemAxon
Polarizability8.74 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
DeepCCS[M+H]+120.69830932474
DeepCCS[M-H]-118.18830932474
DeepCCS[M-2H]-154.24130932474
DeepCCS[M+Na]+128.82930932474
AllCCS[M+H]+121.032859911
AllCCS[M+H-H2O]+116.432859911
AllCCS[M+NH4]+125.332859911
AllCCS[M+Na]+126.632859911
AllCCS[M-H]-123.132859911
AllCCS[M+Na-2H]-127.632859911
AllCCS[M+HCOO]-132.632859911

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, 2022.2.88 minutes32390414
Predicted by Siyang on May 30, 202211.4349 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.4 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1449.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid445.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid174.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid322.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid140.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid365.8 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)251.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid943.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid313.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1001.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid316.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid314.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate585.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA441.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water120.2 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1,4-Pentadien-3-oneC=CC(=O)C=C1048.7Standard polar33892256
1,4-Pentadien-3-oneC=CC(=O)C=C649.2Standard non polar33892256
1,4-Pentadien-3-oneC=CC(=O)C=C647.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Pentadien-3-one GC-MS (Non-derivatized) - 70eV, Positivesplash10-0059-9000000000-2d3a327816adb962f2d22021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 1,4-Pentadien-3-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 - 1,4-Pentadien-3-one 10V, Positive-QTOFsplash10-001i-9000000000-ec60ea9a6bd3064daefc2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Pentadien-3-one 20V, Positive-QTOFsplash10-00kr-9000000000-f473deda09b718a9c9b52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Pentadien-3-one 40V, Positive-QTOFsplash10-052r-9000000000-f95f72f318d8879658472021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Pentadien-3-one 10V, Negative-QTOFsplash10-001i-9000000000-e75a5149c7c9bbbbc6e12021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Pentadien-3-one 20V, Negative-QTOFsplash10-053r-9000000000-32458b6626efb624c2452021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 1,4-Pentadien-3-one 40V, Negative-QTOFsplash10-0a4i-9000000000-29ae899f6a00597b9aa12021-10-12Wishart 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 IDNot Available
Chemspider ID472924
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound543199
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. 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 ]