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Showing metabocard for 3-Methylbut-3-enoic acid (HMDB0170858)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2017-10-09 16:50:29 UTC
Update Date2023-02-21 17:33:45 UTC
HMDB IDHMDB0170858
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-Methylbut-3-enoic acid
DescriptionIsopropenylacetic acid belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present. Isopropenylacetic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Data?1677000825
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0170858 (3-Methylbut-3-enoic acid)

      
  Mrv1652311101723262D          

  7  6  0  0  0  0            999 V2000
   -2.1873    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9017    0.5580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1873    1.7955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4728    0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7583    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7583    1.7955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0439    0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  1  1  0  0  0  0
  1  3  2  0  0  0  0
M  END
Download

3D MOL for HMDB0170858 (3-Methylbut-3-enoic acid)

HMDB0170858
     RDKit          3D
3-Methylbut-3-enoic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.1449   -1.1040    0.9858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6736   -0.0887    0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3559    0.3395   -0.9382 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5590    0.6125    0.7764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5439    0.4898   -0.3351 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8745    1.5522   -0.9702 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0741   -0.7452   -0.6554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0317   -1.6007    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6265   -1.4010    1.8961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7588   -0.0553   -1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4094   -0.0555   -0.9960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021    1.4225   -1.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3373    1.6615    1.0078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0103    0.0487    1.6253 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0036   -1.0762   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for HMDB0170858 (3-Methylbut-3-enoic acid)

      
  Mrv1652311101723262D          

  7  6  0  0  0  0            999 V2000
   -2.1873    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9017    0.5580    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1873    1.7955    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4728    0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7583    0.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7583    1.7955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0439    0.5580    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  2  1  1  0  0  0  0
  1  3  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0170858

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h1,3H2,2H3,(H,6,7)

> <INCHI_KEY>
IGRURXZWJCSNKU-UHFFFAOYSA-N

> <FORMULA>
C5H8O2

> <MOLECULAR_WEIGHT>
100.117

> <EXACT_MASS>
100.052429498

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.253514360110143

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbut-3-enoic acid

> <ALOGPS_LOGP>
0.80

> <JCHEM_LOGP>
0.861132083

> <ALOGPS_LOGS>
0.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.829624564016336

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
26.197699999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isopropenylacetic acid

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0170858 (3-Methylbut-3-enoic acid)

HMDB0170858
     RDKit          3D
3-Methylbut-3-enoic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -1.1449   -1.1040    0.9858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6736   -0.0887    0.2923 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3559    0.3395   -0.9382 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5590    0.6125    0.7764 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5439    0.4898   -0.3351 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8745    1.5522   -0.9702 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0741   -0.7452   -0.6554 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0317   -1.6007    0.6216 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6265   -1.4010    1.8961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7588   -0.0553   -1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4094   -0.0555   -0.9960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4021    1.4225   -1.0371 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3373    1.6615    1.0078 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0103    0.0487    1.6253 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0036   -1.0762   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  3 10  1  0
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0170858 (3-Methylbut-3-enoic acid)

HEADER    PROTEIN                                 10-NOV-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-NOV-17         0                                  
HETATM    1  C   UNK     0      -4.083   1.812   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.417   1.042   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -4.083   3.352   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.749   1.042   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.415   1.812   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.415   3.352   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.082   1.042   0.000  0.00  0.00           C+0
CONECT    1    4    2    3                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0170858 (3-Methylbut-3-enoic acid)

COMPND    HMDB0170858
HETATM    1  C1  UNL     1      -1.145  -1.104   0.986  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.674  -0.089   0.292  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.356   0.340  -0.938  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.559   0.612   0.776  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.544   0.490  -0.335  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.875   1.552  -0.970  1.00  0.00           O  
HETATM    7  O2  UNL     1       2.074  -0.745  -0.655  1.00  0.00           O  
HETATM    8  H1  UNL     1      -2.032  -1.601   0.622  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.627  -1.401   1.896  1.00  0.00           H  
HETATM   10  H3  UNL     1      -0.759  -0.055  -1.818  1.00  0.00           H  
HETATM   11  H4  UNL     1      -2.409  -0.056  -0.996  1.00  0.00           H  
HETATM   12  H5  UNL     1      -1.402   1.422  -1.037  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.337   1.661   1.008  1.00  0.00           H  
HETATM   14  H7  UNL     1       1.010   0.049   1.625  1.00  0.00           H  
HETATM   15  H8  UNL     1       3.004  -1.076  -0.455  1.00  0.00           H  
CONECT    1    2    2    8    9
CONECT    2    3    4
CONECT    3   10   11   12
CONECT    4    5   13   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for HMDB0170858 (3-Methylbut-3-enoic acid)

CC(=C)CC(O)=O
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INCHI for HMDB0170858 (3-Methylbut-3-enoic acid)

InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h1,3H2,2H3,(H,6,7)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
IsopropenylacetateGenerator
3-​methylvinylacetic acidSMPDB, HMDB
3-​methylene-butanoic acidSMPDB, HMDB
3-methyl-3-butenoic acidSMPDB, HMDB
3-Methylbut-3-enoateGenerator
Chemical FormulaC5H8O2
Average Molecular Weight100.117
Monoisotopic Molecular Weight100.052429498
IUPAC Name3-methylbut-3-enoic acid
Traditional Nameisopropenylacetic acid
CAS Registry Number1617-31-8
SMILES
CC(=C)CC(O)=O
InChI Identifier
InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h1,3H2,2H3,(H,6,7)
InChI KeyIGRURXZWJCSNKU-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as methyl-branched fatty acids. These are fatty acids with an acyl chain that has a methyl branch. Usually, they are saturated and contain only one or more methyl group. However, branches other than methyl may be present.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMethyl-branched fatty acids
Alternative Parents
Substituents
  • Methyl-branched fatty acid
  • Unsaturated fatty acid
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP0.8ALOGPS
logP0.86ChemAxon
logS0ALOGPS
pKa (Strongest Acidic)4.83ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity26.2 m³·mol⁻¹ChemAxon
Polarizability10.25 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]-123.21231661259
AllCCS[M+H]+124.40731661259
DeepCCS[M+H]+129.41630932474
DeepCCS[M-H]-126.65530932474
DeepCCS[M-2H]-162.97430932474
DeepCCS[M+Na]+137.83830932474
AllCCS[M+H]+124.432859911
AllCCS[M+H-H2O]+120.132859911
AllCCS[M+NH4]+128.532859911
AllCCS[M+Na]+129.632859911
AllCCS[M-H]-123.232859911
AllCCS[M+Na-2H]-127.132859911
AllCCS[M+HCOO]-131.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Methylbut-3-enoic acidCC(=C)CC(O)=O1644.1Standard polar33892256
3-Methylbut-3-enoic acidCC(=C)CC(O)=O844.3Standard non polar33892256
3-Methylbut-3-enoic acidCC(=C)CC(O)=O890.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Methylbut-3-enoic acid,1TMS,isomer #1C=C(C)CC(=O)O[Si](C)(C)C948.9Semi standard non polar33892256
3-Methylbut-3-enoic acid,1TBDMS,isomer #1C=C(C)CC(=O)O[Si](C)(C)C(C)(C)C1158.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylbut-3-enoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0k9f-9000000000-3dfa14231be969307d142018-04-09Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylbut-3-enoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Methylbut-3-enoic acid 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 - 3-Methylbut-3-enoic acid 10V, Positive-QTOFsplash10-001i-9200000000-60e1c1aebd5372da59eb2018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 20V, Positive-QTOFsplash10-0a4l-9000000000-29bc33769a3b2f751f672018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 40V, Positive-QTOFsplash10-0a4r-9000000000-9ae54a814fcd167b47b42018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 10V, Negative-QTOFsplash10-052b-9000000000-c265d1766b7b797776ef2018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 20V, Negative-QTOFsplash10-0a5a-9000000000-ff30a8a46167c9aadbc02018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 40V, Negative-QTOFsplash10-0a59-9000000000-e15a364142f5de030c632018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 10V, Negative-QTOFsplash10-0002-9000000000-5289cc75fe7aae11de792021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 20V, Negative-QTOFsplash10-000t-9000000000-665649a7a636b4a18f2b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 40V, Negative-QTOFsplash10-00kf-9000000000-6ee087da280d4e1fbea82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 10V, Positive-QTOFsplash10-000x-9000000000-fe872a6cb1845b29a4c82021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 20V, Positive-QTOFsplash10-052f-9000000000-f61e5c9f6c467f2bb3772021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Methylbut-3-enoic acid 40V, Positive-QTOFsplash10-000l-9000000000-fd325c57365f4f34ff7a2021-09-22Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified3-hydroxy-3-methylglutaryl-CoA Lyase Deficiency details
Associated Disorders and Diseases
Disease References
3-Hydroxy-3-methylglutaryl-CoA lyase deficiency
  1. Jakobs C, Bojasch M, Duran M, Ketting D, Wadman SK, Leupold D: 3-methyl-3-butenoic acid: an artefact in the urinary metabolic pattern of patients with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency. Clin Chim Acta. 1980 Sep 8;106(1):85-9. [PubMed:6157502 ]
Associated OMIM IDs
  • 246450 (3-Hydroxy-3-methylglutaryl-CoA lyase deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
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. Jakobs C, Bojasch M, Duran M, Ketting D, Wadman SK, Leupold D: 3-methyl-3-butenoic acid: an artefact in the urinary metabolic pattern of patients with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency. Clin Chim Acta. 1980 Sep 8;106(1):85-9. [PubMed:6157502 ]