Hmdb loader

Showing metabocard for trans-2-pentenal (HMDB0304502)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 10:16:34 UTC
Update Date2021-09-24 10:16:34 UTC
HMDB IDHMDB0304502
Secondary Accession NumbersNone
Metabolite Identification
Common Nametrans-2-pentenal
DescriptionTrans-2-pentenal, also known as 3-ethyl-2-propenal or 3-ethylacrolein, is a member of the class of compounds known as enals. Enals are an alpha,beta-unsaturated aldehyde of general formula RC=C-CH=O in which the aldehydic C=O function is conjugated to a C=C triple bond at the alpha,beta position. Trans-2-pentenal is soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Trans-2-pentenal can be found in a number of food items such as fruits, swiss chard, giant butterbur, and pear, which makes trans-2-pentenal a potential biomarker for the consumption of these food products.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0304502 (trans-2-pentenal)


  Mrv1533004201500142D          

  6  5  0  0  0  0            999 V2000
    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    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 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
Download

3D MOL for HMDB0304502 (trans-2-pentenal)

HMDB0304502
     RDKit          3D
trans-2-pentenal
 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.8256    0.1895    0.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7375    0.3713   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1252   -0.8128   -0.5192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4017   -0.7704   -0.2942 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1106    0.4173    0.1006 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3691    0.3464    0.2952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5138   -0.4575    1.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0638    1.1956    1.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7424   -0.1491    0.1563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2091    1.3146   -0.1993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2300    0.4957   -1.3870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3130   -1.7747   -0.8161 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9545   -1.7250   -0.4224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6742    1.3590    0.2463 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
M  END
Download

3D SDF for HMDB0304502 (trans-2-pentenal)


  Mrv1533004201500142D          

  6  5  0  0  0  0            999 V2000
    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    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 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  4  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0304502

> <DATABASE_NAME>
hmdb

> <SMILES>
CCC=CC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O/c1-2-3-4-5-6/h3-5H,2H2,1H3

> <INCHI_KEY>
DTCCTIQRPGSLPT-UHFFFAOYSA-N

> <FORMULA>
C5H8O

> <MOLECULAR_WEIGHT>
84.118

> <EXACT_MASS>
84.057514878

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
9.661209394158462

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pent-2-enal

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
1.2055346999999996

> <ALOGPS_LOGS>
-0.72

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.180923009082911

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
26.640500000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.62e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-pentenal

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0304502 (trans-2-pentenal)

HMDB0304502
     RDKit          3D
trans-2-pentenal
 14 13  0  0  0  0  0  0  0  0999 V2000
   -1.8256    0.1895    0.6442 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7375    0.3713   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1252   -0.8128   -0.5192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4017   -0.7704   -0.2942 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1106    0.4173    0.1006 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3691    0.3464    0.2952 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5138   -0.4575    1.4880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0638    1.1956    1.0981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7424   -0.1491    0.1563 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2091    1.3146   -0.1993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2300    0.4957   -1.3870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3130   -1.7747   -0.8161 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9545   -1.7250   -0.4224 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6742    1.3590    0.2463 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  3
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  4 13  1  0
  5 14  1  0
M  END
Download

PDB for HMDB0304502 (trans-2-pentenal)

HEADER    PROTEIN                                 20-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-15         0                                  
HETATM    1  C   UNK     0       3.850   1.334   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   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000  -2.667   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
Download

3D PDB for HMDB0304502 (trans-2-pentenal)

COMPND    HMDB0304502
HETATM    1  C1  UNL     1      -1.826   0.189   0.644  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.738   0.371  -0.391  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.125  -0.813  -0.519  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.402  -0.770  -0.294  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.111   0.417   0.101  1.00  0.00           C  
HETATM    6  O1  UNL     1       3.369   0.346   0.295  1.00  0.00           O  
HETATM    7  H1  UNL     1      -1.514  -0.458   1.488  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.064   1.196   1.098  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.742  -0.149   0.156  1.00  0.00           H  
HETATM   10  H4  UNL     1      -0.209   1.315  -0.199  1.00  0.00           H  
HETATM   11  H5  UNL     1      -1.230   0.496  -1.387  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.313  -1.775  -0.816  1.00  0.00           H  
HETATM   13  H7  UNL     1       1.954  -1.725  -0.422  1.00  0.00           H  
HETATM   14  H8  UNL     1       1.674   1.359   0.246  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4    4   12
CONECT    4    5   13
CONECT    5    6    6   14
END
Download

SMILES for HMDB0304502 (trans-2-pentenal)

CCC=CC=O
Download

INCHI for HMDB0304502 (trans-2-pentenal)

InChI=1S/C5H8O/c1-2-3-4-5-6/h3-5H,2H2,1H3
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
3-Ethyl-2-propenalChEBI
3-EthylacroleinChEBI
3-Ethylprop-2-enalChEBI
beta-Aethyl-acroleinChEBI
gamma-MethylcrotonaldehydeChEBI
PropylidenacetaldehydChEBI
b-Aethyl-acroleinGenerator
Β-aethyl-acroleinGenerator
g-MethylcrotonaldehydeGenerator
Γ-methylcrotonaldehydeGenerator
2-Pentenal, (e)-isomerMeSH
2-PentenalMeSH
Chemical FormulaC5H8O
Average Molecular Weight84.118
Monoisotopic Molecular Weight84.057514878
IUPAC Namepent-2-enal
Traditional Name2-pentenal
CAS Registry NumberNot Available
SMILES
CCC=CC=O
InChI Identifier
InChI=1S/C5H8O/c1-2-3-4-5-6/h3-5H,2H2,1H3
InChI KeyDTCCTIQRPGSLPT-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as enals. These are an alpha,beta-unsaturated aldehyde of general formula RC=C-CH=O in which the aldehydic C=O function is conjugated to a C=C triple bond at the alpha,beta position.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentEnals
Alternative Parents
Substituents
  • Enal
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Source
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
logP1.25ALOGPS
logP1.21ChemAxon
logS-0.72ALOGPS
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area17.07 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.64 m³·mol⁻¹ChemAxon
Polarizability9.66 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
AllCCS[M+H]+121.66232859911
AllCCS[M+H-H2O]+117.12732859911
AllCCS[M+Na]+127.1232859911
AllCCS[M+NH4]+125.89732859911
AllCCS[M-H]-128.70232859911
AllCCS[M+Na-2H]-133.24632859911
AllCCS[M+HCOO]-138.25132859911
DeepCCS[M+H]+123.98830932474
DeepCCS[M-H]-121.65230932474
DeepCCS[M-2H]-157.63830932474
DeepCCS[M+Na]+132.08630932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202212.7722 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.99 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1590.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid443.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid184.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid335.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid137.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid493.3 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 Acid546.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)196.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1018.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid362.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1161.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid371.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid346.9 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate570.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA461.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water91.9 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 10V, Positive-QTOFsplash10-000i-9000000000-77d1a6bd82603d3fdc412015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 20V, Positive-QTOFsplash10-00kr-9000000000-872706e87e4952c78cce2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 40V, Positive-QTOFsplash10-052f-9000000000-e375dfa009ad9a5354bf2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 10V, Negative-QTOFsplash10-001i-9000000000-36b33b6bb3f188e4b79d2015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 20V, Negative-QTOFsplash10-001i-9000000000-35a6ab4c7bf244eabf492015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 40V, Negative-QTOFsplash10-00kf-9000000000-3afd0f52caebce4f8ad42015-05-27Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 10V, Positive-QTOFsplash10-05n0-9000000000-ee082819d4c6021e47602021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 20V, Positive-QTOFsplash10-052o-9000000000-67d99b9dbc142ae0c3f22021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 40V, Positive-QTOFsplash10-00ko-9000000000-a6a17afa3d9a3c74e9e42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 10V, Negative-QTOFsplash10-001i-9000000000-1fe8bbf8f6ab17ae0b2b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 20V, Negative-QTOFsplash10-00lr-9000000000-b09a0e6335e2e6873a632021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - trans-2-pentenal 40V, Negative-QTOFsplash10-014j-9000000000-3b6b08af388ca181a26f2021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB031204
KNApSAcK IDC00011389
Chemspider ID12452
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12993
PDB IDNot Available
ChEBI ID61722
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1457931
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available