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Showing metabocard for 3-Methylpentanoic acid (HMDB0033774)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-09-11 18:32:11 UTC
Update Date2023-02-21 17:23:36 UTC
HMDB IDHMDB0033774
Secondary Accession Numbers
  • HMDB33774
Metabolite Identification
Common Name3-Methylpentanoic acid
Description3-Methylpentanoic acid, also known as 3-methyl-pentanoate or 3-methyl-N-valeric 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. Based on a literature review a significant number of articles have been published on 3-Methylpentanoic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033774 (3-Methylpentanoic acid)

  Mrv0541 02241216162D          

  8  7  0  0  0  0            999 V2000
   -4.2429   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5284   -4.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0994   -4.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705   -4.3165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139   -3.0790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850   -3.0790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  3  7  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
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3D MOL for HMDB0033774 (3-Methylpentanoic acid)

HMDB0033774
     RDKit          3D
3-Methylpentanoic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.8841   -1.2041    0.0104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4785    0.0718   -0.6858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698    0.6216   -0.1435 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1397    1.8572   -0.8796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8233   -0.4635   -0.1347 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1615   -0.1582    0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5834    0.9345    0.7711 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0935   -1.1906    0.3555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2916   -2.0680   -0.3366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9497   -1.3972   -0.2954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8598   -1.0625    1.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3097    0.7899   -0.5477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3973   -0.1090   -1.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4005    0.9027    0.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0521    2.3921   -0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1048    1.6339   -1.9823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6987    2.5689   -0.7096 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4208   -1.3058    0.4686 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9424   -0.8856   -1.1685 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1180   -1.9282   -0.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
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3D SDF for HMDB0033774 (3-Methylpentanoic acid)

  Mrv0541 02241216162D          

  8  7  0  0  0  0            999 V2000
   -4.2429   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5284   -4.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0994   -4.3165    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850   -3.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6705   -4.3165    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8139   -3.0790    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3850   -3.0790    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  3  7  1  0  0  0  0
  5  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033774

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O2/c1-3-5(2)4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)

> <INCHI_KEY>
IGIDLTISMCAULB-UHFFFAOYSA-N

> <FORMULA>
C6H12O2

> <MOLECULAR_WEIGHT>
116.1583

> <EXACT_MASS>
116.083729628

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
12.959751216551123

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-methylpentanoic acid

> <ALOGPS_LOGP>
1.82

> <JCHEM_LOGP>
1.6533465589999996

> <ALOGPS_LOGS>
-0.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.086507461266978

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
31.0212

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-methyl valeric acid

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0033774 (3-Methylpentanoic acid)

HMDB0033774
     RDKit          3D
3-Methylpentanoic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -1.8841   -1.2041    0.0104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4785    0.0718   -0.6858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1698    0.6216   -0.1435 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1397    1.8572   -0.8796 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8233   -0.4635   -0.1347 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1615   -0.1582    0.3509 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5834    0.9345    0.7711 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0935   -1.1906    0.3555 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2916   -2.0680   -0.3366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9497   -1.3972   -0.2954 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8598   -1.0625    1.1110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3097    0.7899   -0.5477 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3973   -0.1090   -1.7749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4005    0.9027    0.9272 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0521    2.3921   -0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1048    1.6339   -1.9823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6987    2.5689   -0.7096 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4208   -1.3058    0.4686 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9424   -0.8856   -1.1685 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1180   -1.9282   -0.3305 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  4 17  1  0
  5 18  1  0
  5 19  1  0
  8 20  1  0
M  END
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PDB for HMDB0033774 (3-Methylpentanoic acid)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -7.920  -7.287   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.586  -8.057   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.253  -7.287   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.919  -8.057   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.585  -7.287   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.252  -8.057   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.253  -5.747   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.585  -5.747   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    8                                                  
CONECT    6    5                                                            
CONECT    7    3                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0033774 (3-Methylpentanoic acid)

COMPND    HMDB0033774
HETATM    1  C1  UNL     1      -1.884  -1.204   0.010  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.479   0.072  -0.686  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.170   0.622  -0.144  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.140   1.857  -0.880  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.823  -0.464  -0.135  1.00  0.00           C  
HETATM    6  C6  UNL     1       2.161  -0.158   0.351  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.583   0.935   0.771  1.00  0.00           O  
HETATM    8  O2  UNL     1       3.094  -1.191   0.355  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.292  -2.068  -0.337  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.950  -1.397  -0.295  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.860  -1.062   1.111  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.310   0.790  -0.548  1.00  0.00           H  
HETATM   13  H5  UNL     1      -1.397  -0.109  -1.775  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.400   0.903   0.927  1.00  0.00           H  
HETATM   15  H7  UNL     1       1.052   2.392  -0.590  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.105   1.634  -1.982  1.00  0.00           H  
HETATM   17  H9  UNL     1      -0.699   2.569  -0.710  1.00  0.00           H  
HETATM   18  H10 UNL     1       0.421  -1.306   0.469  1.00  0.00           H  
HETATM   19  H11 UNL     1       0.942  -0.886  -1.169  1.00  0.00           H  
HETATM   20  H12 UNL     1       3.118  -1.928  -0.330  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4    5   14
CONECT    4   15   16   17
CONECT    5    6   18   19
CONECT    6    7    7    8
CONECT    8   20
END
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SMILES for HMDB0033774 (3-Methylpentanoic acid)

CCC(C)CC(O)=O
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INCHI for HMDB0033774 (3-Methylpentanoic acid)

InChI=1S/C6H12O2/c1-3-5(2)4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H12O2
Average Molecular Weight116.1583
Monoisotopic Molecular Weight116.083729628
IUPAC Name3-methylpentanoic acid
Traditional Name3-methyl valeric acid
CAS Registry Number105-43-1
SMILES
CCC(C)CC(O)=O
InChI Identifier
InChI=1S/C6H12O2/c1-3-5(2)4-6(7)8/h5H,3-4H2,1-2H3,(H,7,8)
InChI KeyIGIDLTISMCAULB-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
  • 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 locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point196.00 to 198.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility5266 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP1.560 (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
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified717.412 (28.696-2553.986) nmol/g wet fecesChildren (1 - 13 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected and Quantified1119.162 (57.393-5423.633) nmol/g wet fecesChildren (1 - 13 years old)Both
Autism		 details
FecesDetected and Quantified1176.555 (57.393-6657.581) nmol/g wet fecesChildren (1 - 13 years old)Both
Developmental Disorder Not Otherwise Specified		 details
Associated Disorders and Diseases
Disease References
Autism
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Pervasive developmental disorder not otherwise specified
  1. De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R: Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One. 2013 Oct 9;8(10):e76993. doi: 10.1371/journal.pone.0076993. eCollection 2013. [PubMed:24130822 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012545
KNApSAcK IDC00017925
Chemspider ID7469
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound7755
PDB IDNot Available
ChEBI ID166883
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1028581
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.