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Showing metabocard for 2-Butenoic acid methyl ester (HMDB0302473)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 18:03:07 UTC
Update Date2021-09-23 18:03:07 UTC
HMDB IDHMDB0302473
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-Butenoic acid methyl ester
Description2-butenoic acid methyl ester is a member of the class of compounds known as fatty acid esters. Fatty acid esters are carboxylic ester derivatives of a fatty acid. 2-butenoic acid methyl ester is soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). 2-butenoic acid methyl ester can be found in papaya, which makes 2-butenoic acid methyl ester a potential biomarker for the consumption of this food product.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302473 (2-Butenoic acid methyl ester)


  Mrv1533007131513362D          

  9  8  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
   -1.6500   -1.4289    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
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
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3D MOL for HMDB0302473 (2-Butenoic acid methyl ester)

HMDB0302473
     RDKit          3D
2-Butenoic acid methyl ester
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.9718   -0.3770   -0.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6729    0.3612   -0.0454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5552   -0.3448    0.0795 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7487    0.3164    0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8291    1.5572    0.1106 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8842   -0.4349    0.2875 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1914    0.0977    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8074    0.3394   -0.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1059   -0.9699    0.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9586   -1.1259   -0.9529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327    1.4468   -0.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6376   -1.4232    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2832    1.1129   -0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8468   -0.5965   -0.2069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5587    0.0408    1.4265 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0302473 (2-Butenoic acid methyl ester)


  Mrv1533007131513362D          

  9  8  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
   -1.6500   -1.4289    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
   -1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  3  2  0  0  0  0
  5  4  1  0  0  0  0
  6  5  2  0  0  0  0
  7  2  1  0  0  0  0
  7  5  1  0  0  0  0
  8  3  1  0  0  0  0
  9  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302473

> <DATABASE_NAME>
hmdb

> <SMILES>
[H]\C(C)=C(\[H])C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O2/c1-3-4-5(6)7-2/h3-4H,1-2H3/b4-3+

> <INCHI_KEY>
MCVVUJPXSBQTRZ-ONEGZZNKSA-N

> <FORMULA>
C5H8O2

> <MOLECULAR_WEIGHT>
100.117

> <EXACT_MASS>
100.052429498

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.614017510142286

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (2E)-but-2-enoate

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
1.2988096766666664

> <ALOGPS_LOGS>
-0.54

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.782766825407376

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
27.734

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2E)-but-2-enoate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0302473 (2-Butenoic acid methyl ester)

HMDB0302473
     RDKit          3D
2-Butenoic acid methyl ester
 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.9718   -0.3770   -0.1211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6729    0.3612   -0.0454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5552   -0.3448    0.0795 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7487    0.3164    0.1591 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8291    1.5572    0.1106 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8842   -0.4349    0.2875 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1914    0.0977    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8074    0.3394   -0.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1059   -0.9699    0.8293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9586   -1.1259   -0.9529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6327    1.4468   -0.0903 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6376   -1.4232    0.1206 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2832    1.1129   -0.0241 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8468   -0.5965   -0.2069 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5587    0.0408    1.4265 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  4  6  1  0
  6  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  3 12  1  0
  7 13  1  0
  7 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0302473 (2-Butenoic acid methyl ester)

HEADER    PROTEIN                                 13-JUL-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-JUL-15         0                                  
HETATM    1  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.080  -2.667   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
HETATM    7  O   UNK     0      -2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  H   UNK     0       2.310  -1.334   0.000  0.00  0.00           H+0
HETATM    9  H   UNK     0      -0.770   1.334   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    7                                                            
CONECT    3    1    4    8                                                  
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    2    5                                                       
CONECT    8    3                                                            
CONECT    9    4                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0302473 (2-Butenoic acid methyl ester)

COMPND    HMDB0302473
HETATM    1  C1  UNL     1      -2.972  -0.377  -0.121  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.673   0.361  -0.045  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.555  -0.345   0.080  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.749   0.316   0.159  1.00  0.00           C  
HETATM    5  O1  UNL     1       0.829   1.557   0.111  1.00  0.00           O  
HETATM    6  O2  UNL     1       1.884  -0.435   0.287  1.00  0.00           O  
HETATM    7  C5  UNL     1       3.191   0.098   0.373  1.00  0.00           C  
HETATM    8  H1  UNL     1      -3.807   0.339  -0.248  1.00  0.00           H  
HETATM    9  H2  UNL     1      -3.106  -0.970   0.829  1.00  0.00           H  
HETATM   10  H3  UNL     1      -2.959  -1.126  -0.953  1.00  0.00           H  
HETATM   11  H4  UNL     1      -1.633   1.447  -0.090  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.638  -1.423   0.121  1.00  0.00           H  
HETATM   13  H6  UNL     1       3.283   1.113  -0.024  1.00  0.00           H  
HETATM   14  H7  UNL     1       3.847  -0.597  -0.207  1.00  0.00           H  
HETATM   15  H8  UNL     1       3.559   0.041   1.427  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    3   11
CONECT    3    4   12
CONECT    4    5    5    6
CONECT    6    7
CONECT    7   13   14   15
END
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SMILES for HMDB0302473 (2-Butenoic acid methyl ester)

[H]\C(C)=C(\[H])C(=O)OC
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INCHI for HMDB0302473 (2-Butenoic acid methyl ester)

InChI=1S/C5H8O2/c1-3-4-5(6)7-2/h3-4H,1-2H3/b4-3+
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Methyl crotonic acidGenerator
2-Butenoate methyl esterGenerator
Chemical FormulaC5H8O2
Average Molecular Weight100.117
Monoisotopic Molecular Weight100.052429498
IUPAC Namemethyl (2E)-but-2-enoate
Traditional Namemethyl (2E)-but-2-enoate
CAS Registry NumberNot Available
SMILES
[H]\C(C)=C(\[H])C(=O)OC
InChI Identifier
InChI=1S/C5H8O2/c1-3-4-5(6)7-2/h3-4H,1-2H3/b4-3+
InChI KeyMCVVUJPXSBQTRZ-ONEGZZNKSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as fatty acid esters. These are carboxylic ester derivatives of a fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acid esters
Direct ParentFatty acid esters
Alternative Parents
Substituents
  • Fatty acid ester
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Methyl ester
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP1.3ChemAxon
logS-0.54ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity27.73 m³·mol⁻¹ChemAxon
Polarizability10.61 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]+125.22332859911
AllCCS[M+H-H2O]+120.81432859911
AllCCS[M+Na]+130.52632859911
AllCCS[M+NH4]+129.33832859911
AllCCS[M-H]-125.0932859911
AllCCS[M+Na-2H]-128.98332859911
AllCCS[M+HCOO]-133.27932859911
DeepCCS[M+H]+120.44330932474
DeepCCS[M-H]-116.86530932474
DeepCCS[M-2H]-154.63730932474
DeepCCS[M+Na]+130.12630932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 10V, Positive-QTOFsplash10-0uxr-9600000000-7b568f652434d28cae052016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 20V, Positive-QTOFsplash10-0uxr-9300000000-31d4f712ef520f1281912016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 40V, Positive-QTOFsplash10-0f6x-9000000000-62b0c40b21438c9dd1fe2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 10V, Negative-QTOFsplash10-0002-9000000000-1e220427f19d1fa70c082016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 20V, Negative-QTOFsplash10-00kb-9000000000-0a15578a5dc1c883b6b42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 40V, Negative-QTOFsplash10-014i-9000000000-c5ab30e3dbcd15ff99b42016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 10V, Positive-QTOFsplash10-00kf-9100000000-131755e46cf3e2015f5d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 20V, Positive-QTOFsplash10-0a4l-9000000000-34fdd53e7f12fc991f9b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 40V, Positive-QTOFsplash10-0006-9000000000-f7dfac97b795b46f91ba2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 10V, Negative-QTOFsplash10-014j-9000000000-caef9147f9ceb5a6c1fd2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 20V, Negative-QTOFsplash10-014i-9000000000-b84b0be2588faef28a8b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Butenoic acid methyl ester 40V, Negative-QTOFsplash10-014l-9000000000-25a169168e33ef05621f2021-10-21Wishart 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 IDFDB004707
KNApSAcK IDNot Available
Chemspider ID553692
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound638132
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 ReferencesNot Available