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Showing NP-Card for Senecioic acid (NP0000070)

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Record Information
Version1.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-19 20:22:32 UTC
NP-MRD IDNP0000070
Secondary Accession NumbersNone
Natural Product 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 NP0000070 (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
Download

3D MOL for NP0000070 (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
Download

3D SDF for NP0000070 (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>
NP0000070

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
Download

3D-SDF for NP0000070 (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 NP0000070 (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 NP0000070 (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 NP0000070 (Senecioic acid)

CC(C)=CC(O)=O
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INCHI for NP0000070 (Senecioic acid)

InChI=1S/C5H8O2/c1-4(2)3-5(6)7/h3H,1-2H3,(H,6,7)
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View in JSmol
Synonyms
ValueSource
3,3-Dimethylacrylic acidChEBI
3-Methyl-2-butenoic acidChEBI
3-Methylcrotonic acidChEBI
beta,beta-Dimethacrylic acidChEBI
beta,beta-Dimethylacrylic acidChEBI
beta-Methylcrotonic acidChEBI
SENECIC ACIDChEBI
3,3-DimethylacrylateGenerator
3-Methyl-2-butenoateGenerator
3-MethylcrotonateGenerator
b,b-DimethacrylateGenerator
b,b-Dimethacrylic acidGenerator
beta,beta-DimethacrylateGenerator
Β,β-dimethacrylateGenerator
Β,β-dimethacrylic acidGenerator
b,b-DimethylacrylateGenerator
b,b-Dimethylacrylic acidGenerator
beta,beta-DimethylacrylateGenerator
Β,β-dimethylacrylateGenerator
Β,β-dimethylacrylic acidGenerator
b-MethylcrotonateGenerator
b-Methylcrotonic acidGenerator
beta-MethylcrotonateGenerator
Β-methylcrotonateGenerator
Β-methylcrotonic acidGenerator
SENECateGenerator
SenecioateGenerator
3-Methyl-crotonateHMDB
3-Methyl-crotonic acidHMDB
3-Methylbut-2-enoateHMDB
3-Methylbut-2-enoic acidHMDB
b,b-Dimethyl acrylateHMDB
b,b-Dimethyl acrylic acidHMDB
beta,beta-Dimethyl acrylateHMDB
Β,β-dimethyl acrylateHMDB
Β,β-dimethyl acrylic acidHMDB
Senecioic acidChEBI
Chemical FormulaC5H8O2
Average Mass100.1158 Da
Monoisotopic Mass100.05243 Da
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
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Farfugium japonicumLOTUS Database
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
Peucedanum japonicumKNApSAcK Database
PhasianidaeFooDB
Phasianus colchicusFooDB
Senecio magnificusLOTUS Database
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
Vitis viniferaLOTUS Database
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point65 °CNot Available
Boiling Point197 °Chttps://pubchem.ncbi.nlm.nih.gov/compound/3_3-Dimethylacrylic-acid#section=Melting-Point
Water Solubility10 mg/mLNot Available
LogP1.350 (est)The Good Scents Company Information System
Predicted Properties
PropertyValueSource
Water Solubility71.1 g/LALOGPS
logP0.79ALOGPS
logP1.16ChemAxon
logS-0.15ALOGPS
pKa (Strongest Acidic)5.02ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity27.25 m³·mol⁻¹ChemAxon
Polarizability10.25 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000509
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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
Good Scents IDrw1035401
References
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. Farine JP, Sirugue D, Abed-Vieillard D, Everaerts C, Le Quere JL, Bonnard O, Brossut R: The male abdominal glands of Leucophaea maderae: chemical identification of the volatile secretion and sex pheromone function. J Chem Ecol. 2007 Feb;33(2):405-15. doi: 10.1007/s10886-006-9224-7. Epub 2007 Jan 3. [PubMed:17200891 ]
  5. Joglekar SS, Dhavlikar RS: Microbial transformation of terpenoids. I. Identification of metabolites produced by a pseudomonad from citronellal and citral. Appl Microbiol. 1969 Dec;18(6):1084-7. doi: 10.1128/am.18.6.1084-1087.1969. [PubMed:5370660 ]
  6. 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. doi: 10.1016/0009-8981(80)90377-0. [PubMed:6157502 ]