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Showing metabocard for Senecioic acid (HMDB0000509)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:53 UTC
HMDB IDHMDB0000509
Secondary Accession Numbers
  • HMDB00509
Metabolite Identification
Common NameSenecioic acid
DescriptionSenecioic acid, also known as 3-methylcrotonate, 3-methylcrotonic acid or 3,3-dimethylacrylic 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 (however senecioic acid is unsaturated) and contain only one or more methyl group. However, branches other than methyl may be present. Senecioic acid is a methyl-branched fatty acid that has a but-2-enoic acid skeleton bearing a methyl substituent at position 3. Senecioic acid is an unsaturated fatty acid found in the pheromones of mealybug species, the Madeira cockroach and the Southern long-nosed bat. It also appears in the urine of patients with 3-Methylcrotonic aciduria caused by 3-hydroxy-3-methylglutaryl-CoA lyase deficiency (PMID: 6157502 ) and those with 3-Hydroxy-3-methylglutaric aciduria (PMID: 947633 ). The appearance of 3-methylcrotonic acid in urine indicates a blockage in the sixth step of leucine catabolism, which is the cleavage of 3-hydroxy-3-methylglutaryl-CoA to acetoacetic acid and acetyl-CoA.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000509 (Senecioic acid)

  Mrv1652305271900292D          

  7  6  0  0  0  0            999 V2000
   11.2908   -7.3772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0053   -8.6148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1487   -7.3772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4343   -8.6148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0053   -7.7897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4343   -7.7897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7198   -7.3772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
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3D MOL for HMDB0000509 (Senecioic acid)

HMDB0000509
     RDKit          3D
Senecioic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.6627   -0.9946   -0.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0099   -0.2707    0.4977 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1131   -0.9261    1.8021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4449    0.9317    0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3756    1.6737   -0.9517 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8387    2.8219   -1.0480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2172    1.0902   -2.0549 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0410   -1.9942   -0.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0145   -1.1500   -1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.4103   -0.9055 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3390   -2.0203    1.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7740   -0.7735    2.4666 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9779   -0.5283    2.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9247    1.4239    1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    1.1267   -2.9757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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3D SDF for HMDB0000509 (Senecioic acid)

  Mrv1652305271900292D          

  7  6  0  0  0  0            999 V2000
   11.2908   -7.3772    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0053   -8.6148    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1487   -7.3772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4343   -8.6148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0053   -7.7897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4343   -7.7897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7198   -7.3772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  5  2  0  0  0  0
  3  6  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000509

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h3H,1-2H3,(H,6,7)

> <INCHI_KEY>
YYPNJNDODFVZLE-UHFFFAOYSA-N

> <FORMULA>
C5H8O2

> <MOLECULAR_WEIGHT>
100.1158

> <EXACT_MASS>
100.0524295

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.254334993370383

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylbut-2-enoic acid

> <ALOGPS_LOGP>
0.79

> <JCHEM_LOGP>
1.162943559

> <ALOGPS_LOGS>
-0.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.0217490078951394

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
27.2469

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.11e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β,β-dimethacrylate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0000509 (Senecioic acid)

HMDB0000509
     RDKit          3D
Senecioic acid
 15 14  0  0  0  0  0  0  0  0999 V2000
   -0.6627   -0.9946   -0.6044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0099   -0.2707    0.4977 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1131   -0.9261    1.8021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4449    0.9317    0.2991 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3756    1.6737   -0.9517 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8387    2.8219   -1.0480 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2172    1.0902   -2.0549 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0410   -1.9942   -0.2997 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0145   -1.1500   -1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5671   -0.4103   -0.9055 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3390   -2.0203    1.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7740   -0.7735    2.4666 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9779   -0.5283    2.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9247    1.4239    1.1645 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2434    1.1267   -2.9757 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  3 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  7 15  1  0
M  END
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PDB for HMDB0000509 (Senecioic acid)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      21.076 -13.771   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      22.410 -16.081   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      26.411 -13.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      25.077 -16.081   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.410 -14.541   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.077 -14.541   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.744 -13.771   0.000  0.00  0.00           C+0
CONECT    1    5                                                            
CONECT    2    5                                                            
CONECT    3    6                                                            
CONECT    4    6                                                            
CONECT    5    1    2    7                                                  
CONECT    6    3    4    7                                                  
CONECT    7    5    6                                                       
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0000509 (Senecioic acid)

COMPND    HMDB0000509
HETATM    1  C1  UNL     1      -0.663  -0.995  -0.604  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.010  -0.271   0.498  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.113  -0.926   1.802  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.445   0.932   0.299  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.376   1.674  -0.952  1.00  0.00           C  
HETATM    6  O1  UNL     1       0.839   2.822  -1.048  1.00  0.00           O  
HETATM    7  O2  UNL     1      -0.217   1.090  -2.055  1.00  0.00           O  
HETATM    8  H1  UNL     1      -1.041  -1.994  -0.300  1.00  0.00           H  
HETATM    9  H2  UNL     1       0.015  -1.150  -1.490  1.00  0.00           H  
HETATM   10  H3  UNL     1      -1.567  -0.410  -0.905  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.339  -2.020   1.692  1.00  0.00           H  
HETATM   12  H5  UNL     1      -0.774  -0.774   2.467  1.00  0.00           H  
HETATM   13  H6  UNL     1       0.978  -0.528   2.408  1.00  0.00           H  
HETATM   14  H7  UNL     1       0.925   1.424   1.164  1.00  0.00           H  
HETATM   15  H8  UNL     1       0.243   1.127  -2.976  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3    4    4
CONECT    3   11   12   13
CONECT    4    5   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for HMDB0000509 (Senecioic acid)

CC(C)=CC(O)=O
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INCHI for HMDB0000509 (Senecioic acid)

InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h3H,1-2H3,(H,6,7)
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View in JSmolView Stereo Labels
Synonyms
Chemical FormulaC5H8O2
Average Molecular Weight100.1158
Monoisotopic Molecular Weight100.0524295
IUPAC Name3-methylbut-2-enoic acid
Traditional Nameβ,β-dimethacrylate
CAS Registry Number541-47-9
SMILES
CC(C)=CC(O)=O
InChI Identifier
InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h3H,1-2H3,(H,6,7)
InChI KeyYYPNJNDODFVZLE-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 effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point65 °CNot Available
Boiling Point195.00 to 197.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility10 mg/mLNot Available
LogP1.350 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
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 IDFDB000736
KNApSAcK IDC00010280
Chemspider ID10468
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5495
PubChem Compound10931
PDB IDNot Available
ChEBI ID37127
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1035401
References
Synthesis ReferenceIordache, Florin; Badica, Sonia; Ionescu, Alina; Badea, Florin. Synthesis of b,b-dimethylacrylic acid and its methyl and ethyl esters. Revistade Chimie (Bucharest, Romania) (1979), 30(7), 629-32.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Wysocki SJ, Wilkinson SP, Hahnel R, Wong CY, Panegyres PK: 3-Hydroxy-3-methylglutaric aciduria, combined with 3-methylglutaconic aciduria. Clin Chim Acta. 1976 Aug 2;70(3):399-406. [PubMed:947633 ]
  2. Duran M, Ketting D, Wadman SK, Jakobs C, Schutgens RB, Veder HA: Organic acid excretion in a patient with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency: facts and artefacts. Clin Chim Acta. 1978 Dec 1;90(2):187-93. [PubMed:719902 ]
  3. Roth K, Cohn R, Yandrasitz J, Preti G, Dodd P, Segal S: Beta-methylcrotonic aciduria associated with lactic acidosis. J Pediatr. 1976 Feb;88(2):229-35. [PubMed:1249684 ]
  4. 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 ]

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Senecioic acid → 3,4,5-trihydroxy-6-[(3-methylbut-2-enoyl)oxy]oxane-2-carboxylic aciddetails