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Showing metabocard for Penta-1,3-diene (HMDB0256243)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 16:34:14 UTC
Update Date2021-09-26 23:11:45 UTC
HMDB IDHMDB0256243
Secondary Accession NumbersNone
Metabolite Identification
Common NamePenta-1,3-diene
Descriptionpenta-1,3-diene belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds. Based on a literature review very few articles have been published on penta-1,3-diene. This compound has been identified in human blood as reported by (PMID: 31557052 ). Penta-1,3-diene is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Penta-1,3-diene 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 HMDB0256243 (Penta-1,3-diene)


  Mrv1533004181503292D          

  5  4  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  4  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
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3D MOL for HMDB0256243 (Penta-1,3-diene)

HMDB0256243
     RDKit          3D
Penta-1,3-diene
 13 12  0  0  0  0  0  0  0  0999 V2000
   -2.3663    0.2372    0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0741    0.2403    0.2798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1521   -0.5714   -0.4917 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1470   -0.5842   -0.2955 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8083    0.2456    0.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7900   -0.3818   -0.7042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114    0.8518    0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6948    0.8764    1.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5599   -1.2000   -1.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8016   -1.2028   -0.8913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8196   -0.1058    0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1675    0.3208    1.6773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    1.2739    0.3356 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  3
  4  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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3D SDF for HMDB0256243 (Penta-1,3-diene)


  Mrv1533004181503292D          

  5  4  0  0  0  0            999 V2000
    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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  4  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0256243

> <DATABASE_NAME>
hmdb

> <SMILES>
CC=CC=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H8/c1-3-5-4-2/h3-5H,1H2,2H3

> <INCHI_KEY>
PMJHHCWVYXUKFD-UHFFFAOYSA-N

> <FORMULA>
C5H8

> <MOLECULAR_WEIGHT>
68.119

> <EXACT_MASS>
68.062600258

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
8.79057042289956

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
penta-1,3-diene

> <ALOGPS_LOGP>
2.65

> <JCHEM_LOGP>
2.0206595846666664

> <ALOGPS_LOGS>
-2.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
25.9679

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-pentadiene

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0256243 (Penta-1,3-diene)

HMDB0256243
     RDKit          3D
Penta-1,3-diene
 13 12  0  0  0  0  0  0  0  0999 V2000
   -2.3663    0.2372    0.0668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0741    0.2403    0.2798 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1521   -0.5714   -0.4917 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1470   -0.5842   -0.2955 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8083    0.2456    0.7535 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7900   -0.3818   -0.7042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0114    0.8518    0.6595 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6948    0.8764    1.0629 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5599   -1.2000   -1.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8016   -1.2028   -0.8913 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8196   -0.1058    0.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1675    0.3208    1.6773 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9048    1.2739    0.3356 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  3
  4  5  1  0
  1  6  1  0
  1  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  5 12  1  0
  5 13  1  0
M  END
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PDB for HMDB0256243 (Penta-1,3-diene)

HEADER    PROTEIN                                 18-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-APR-15         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
MASTER        0    0    0    0    0    0    0    0    5    0    8    0
END
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3D PDB for HMDB0256243 (Penta-1,3-diene)

COMPND    HMDB0256243
HETATM    1  C1  UNL     1      -2.366   0.237   0.067  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.074   0.240   0.280  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.152  -0.571  -0.492  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.147  -0.584  -0.295  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.808   0.246   0.754  1.00  0.00           C  
HETATM    6  H1  UNL     1      -2.790  -0.382  -0.704  1.00  0.00           H  
HETATM    7  H2  UNL     1      -3.011   0.852   0.660  1.00  0.00           H  
HETATM    8  H3  UNL     1      -0.695   0.876   1.063  1.00  0.00           H  
HETATM    9  H4  UNL     1      -0.560  -1.200  -1.271  1.00  0.00           H  
HETATM   10  H5  UNL     1       1.802  -1.203  -0.891  1.00  0.00           H  
HETATM   11  H6  UNL     1       2.820  -0.106   0.981  1.00  0.00           H  
HETATM   12  H7  UNL     1       1.167   0.321   1.677  1.00  0.00           H  
HETATM   13  H8  UNL     1       1.905   1.274   0.336  1.00  0.00           H  
CONECT    1    2    2    6    7
CONECT    2    3    8
CONECT    3    4    4    9
CONECT    4    5   10
CONECT    5   11   12   13
END
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SMILES for HMDB0256243 (Penta-1,3-diene)

CC=CC=C
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INCHI for HMDB0256243 (Penta-1,3-diene)

InChI=1S/C5H8/c1-3-5-4-2/h3-5H,1H2,2H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H8
Average Molecular Weight68.119
Monoisotopic Molecular Weight68.062600258
IUPAC Namepenta-1,3-diene
Traditional Name1,3-pentadiene
CAS Registry NumberNot Available
SMILES
CC=CC=C
InChI Identifier
InChI=1S/C5H8/c1-3-5-4-2/h3-5H,1H2,2H3
InChI KeyPMJHHCWVYXUKFD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkadienes. These are acyclic hydrocarbons that contain exactly two carbon-to-carbon double bonds.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassUnsaturated hydrocarbons
Sub ClassOlefins
Direct ParentAlkadienes
Alternative Parents
Substituents
  • Alkadiene
  • Unsaturated aliphatic hydrocarbon
  • 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
logP2.65ALOGPS
logP2.02ChemAxon
logS-2.2ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity25.97 m³·mol⁻¹ChemAxon
Polarizability8.79 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]+120.83330932474
DeepCCS[M-H]-118.93730932474
DeepCCS[M-2H]-154.43230932474
DeepCCS[M+Na]+128.83830932474
AllCCS[M+H]+116.432859911
AllCCS[M+H-H2O]+111.732859911
AllCCS[M+NH4]+120.832859911
AllCCS[M+Na]+122.132859911
AllCCS[M-H]-128.532859911
AllCCS[M+Na-2H]-134.032859911
AllCCS[M+HCOO]-140.032859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202214.5763 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.74 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1731.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid548.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid224.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid413.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid252.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid498.9 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 Acid529.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)211.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1190.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid423.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1084.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid440.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid402.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate559.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA460.6 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water140.7 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Penta-1,3-dieneCC=CC=C668.1Standard polar33892256
Penta-1,3-dieneCC=CC=C529.2Standard non polar33892256
Penta-1,3-dieneCC=CC=C517.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Penta-1,3-diene GC-MS (Non-derivatized) - 70eV, Positivesplash10-014i-9000000000-d75c5e568bd05c0caa462021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Penta-1,3-diene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart 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 ID14564
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]