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Showing metabocard for Leucinic acid (HMDB0000665)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2022-09-22 18:35:06 UTC
HMDB IDHMDB0000665
Secondary Accession Numbers
  • HMDB00665
Metabolite Identification
Common NameLeucinic acid
DescriptionLeucinic acid, also known as leucic acid, 2-hydroxyisocaproic acid or 2-hydroxy-4-methylvaleric acid, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Leucinic acid is a valeric acid derivative having a hydroxy substituent at the 2-position and a methyl substituent at the 4-position. It is an alpha-hydroxy analogue of leucine and a metabolite of the branched-chain amino acid leucine. Leucinic acid is found in all organisms ranging from bacteria to plants to animals. Leucinic acid has been found in a patient with dihydrolipoyl dehydrogenase (DLD) deficiency (PMID: 6688766 ). DLD deficiency is caused by mutations in the DLD gene and is inherited in an autosomal recessive manner. A common feature of dihydrolipoamide dehydrogenase deficiency is a potentially life-threatening buildup of lactic acid in tissues (lactic acidosis), which can cause nausea, vomiting, severe breathing problems, and an abnormal heartbeat. Neurological problems are also common in this condition; the first symptoms in affected infants are often decreased muscle tone (hypotonia) and extreme tiredness (lethargy). As the problems worsen, affected infants can have difficulty feeding, decreased alertness, and seizures. Liver problems can also occur in dihydrolipoamide dehydrogenase deficiency, ranging from an enlarged liver (hepatomegaly) to life-threatening liver failure. In some affected people, liver disease, which can begin anytime from infancy to adulthood, is the primary symptom. Leucinic acid is also present in the urine of patients with short bowel syndrome (PMID: 4018104 )
Structure
Data?1582752148
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000665 (Leucinic acid)

  Mrv1652305271900192D          

  9  8  0  0  0  0            999 V2000
   19.3041  -14.9261    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7330  -14.1011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186  -12.8636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8751  -14.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5896  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3041  -14.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1606  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8751  -14.9261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000665 (Leucinic acid)

HMDB0000665
     RDKit          3D
Leucinic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.1048    1.1531    0.2064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0190    0.1372    0.5011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395   -1.2191    0.0974 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2218    0.5301   -0.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3261   -0.4427   -0.0046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0321   -1.7460   -0.3772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5713    0.0337   -0.6810 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1874   -0.7181   -1.4565 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0482    1.3106   -0.4513 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7297    1.9459   -0.4591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9724    0.6880   -0.3297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5116    1.6021    1.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8060    0.1911    1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3857   -1.3188   -0.9992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -2.0463    0.6369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6429   -1.1916    0.2845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0276    0.6490   -1.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5650    1.5197    0.1053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5144   -0.4675    1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3632   -2.4156    0.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9016    1.8052    0.4395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for HMDB0000665 (Leucinic acid)

  Mrv1652305271900192D          

  9  8  0  0  0  0            999 V2000
   19.3041  -14.9261    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.7330  -14.1011    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186  -12.8636    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8751  -14.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5896  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.3041  -14.1011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1606  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.8751  -14.9261    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.0186  -13.6886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  6  1  0  0  0  0
  2  9  1  0  0  0  0
  3  9  2  0  0  0  0
  4  5  1  0  0  0  0
  4  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000665

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-4(2)3-5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)

> <INCHI_KEY>
LVRFTAZAXQPQHI-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.1577

> <EXACT_MASS>
132.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.649767203036058

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-4-methylpentanoic acid

> <ALOGPS_LOGP>
0.50

> <JCHEM_LOGP>
0.7822806383333333

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.276112311717824

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.257807082104199

> <JCHEM_PKA_STRONGEST_BASIC>
-3.801045430820605

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.513400000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
leucate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000665 (Leucinic acid)

HMDB0000665
     RDKit          3D
Leucinic acid
 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.1048    1.1531    0.2064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0190    0.1372    0.5011 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5395   -1.2191    0.0974 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2218    0.5301   -0.2619 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3261   -0.4427   -0.0046 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0321   -1.7460   -0.3772 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5713    0.0337   -0.6810 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1874   -0.7181   -1.4565 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0482    1.3106   -0.4513 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7297    1.9459   -0.4591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9724    0.6880   -0.3297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5116    1.6021    1.1369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8060    0.1911    1.5839 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3857   -1.3188   -0.9992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0470   -2.0463    0.6369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6429   -1.1916    0.2845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0276    0.6490   -1.3428 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5650    1.5197    0.1053 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5144   -0.4675    1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3632   -2.4156    0.2693 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9016    1.8052    0.4395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  0
  9 21  1  0
M  END
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PDB for HMDB0000665 (Leucinic 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      36.034 -27.862   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      38.702 -26.322   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      37.368 -24.012   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      33.367 -26.322   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      34.701 -25.552   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.034 -26.322   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      32.033 -25.552   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      33.367 -27.862   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      37.368 -25.552   0.000  0.00  0.00           C+0
CONECT    1    6                                                            
CONECT    2    9                                                            
CONECT    3    9                                                            
CONECT    4    5    7    8                                                  
CONECT    5    4    6                                                       
CONECT    6    1    5    9                                                  
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    2    3    6                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0000665 (Leucinic acid)

COMPND    HMDB0000665
HETATM    1  C1  UNL     1      -2.105   1.153   0.206  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.019   0.137   0.501  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.539  -1.219   0.097  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.222   0.530  -0.262  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.326  -0.443  -0.005  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.032  -1.746  -0.377  1.00  0.00           O  
HETATM    7  C6  UNL     1       2.571   0.034  -0.681  1.00  0.00           C  
HETATM    8  O2  UNL     1       3.187  -0.718  -1.456  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.048   1.311  -0.451  1.00  0.00           O  
HETATM   10  H1  UNL     1      -1.730   1.946  -0.459  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.972   0.688  -0.330  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.512   1.602   1.137  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.806   0.191   1.584  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.386  -1.319  -0.999  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.047  -2.046   0.637  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.643  -1.192   0.285  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.028   0.649  -1.343  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.565   1.520   0.105  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.514  -0.468   1.102  1.00  0.00           H  
HETATM   20  H11 UNL     1       1.363  -2.416   0.269  1.00  0.00           H  
HETATM   21  H12 UNL     1       2.902   1.805   0.439  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4   13
CONECT    3   14   15   16
CONECT    4    5   17   18
CONECT    5    6    7   19
CONECT    6   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for HMDB0000665 (Leucinic acid)

CC(C)CC(O)C(O)=O
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INCHI for HMDB0000665 (Leucinic acid)

InChI=1S/C6H12O3/c1-4(2)3-5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H12O3
Average Molecular Weight132.1577
Monoisotopic Molecular Weight132.07864425
IUPAC Name2-hydroxy-4-methylpentanoic acid
Traditional Nameleucate
CAS Registry Number498-36-2
SMILES
CC(C)CC(O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-4(2)3-5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)
InChI KeyLVRFTAZAXQPQHI-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Hydroxy fatty acid
  • Methyl-branched fatty acid
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • 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
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point76.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Boiling Point249.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility886 mg/mLNot Available
LogP0.522 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0-50 umol/mmol creatinineNewborn (0-30 days old)Both
Normal		 details
UrineDetected and Quantified0.0 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified0-0.39 umol/mmol creatinineAdult (>18 years old)BothNormal
    • Great Plains Labo...
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAsthma details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022171
KNApSAcK IDNot Available
Chemspider ID83753
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5635
PubChem Compound92779
PDB IDNot Available
ChEBI ID59783
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1488981
References
Synthesis ReferenceCamien, Merill N.; Fowler, Audree V.; Dunn, Max S. Production of a-hydroxy fatty acids by two strains of Lactobacillus casei. Archives of Biochemistry and Biophysics (1959), 83 408-18.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Kuhara T, Shinka T, Inoue Y, Matsumoto M, Yoshino M, Sakaguchi Y, Matsumoto I: Studies of urinary organic acid profiles of a patient with dihydrolipoyl dehydrogenase deficiency. Clin Chim Acta. 1983 Sep 30;133(2):133-40. [PubMed:6688766 ]
  2. Jakobs C, Sweetman L, Nyhan WL: Hydroxy acid metabolites of branched-chain amino acids in amniotic fluid. Clin Chim Acta. 1984 Jul 16;140(2):157-66. [PubMed:6467607 ]
  3. Spaapen LJ, Ketting D, Wadman SK, Bruinvis L, Duran M: Urinary D-4-hydroxyphenyllactate, D-phenyllactate and D-2-hydroxyisocaproate, abnormalities of bacterial origin. J Inherit Metab Dis. 1987;10(4):383-90. [PubMed:3126358 ]
  4. Haan E, Brown G, Bankier A, Mitchell D, Hunt S, Blakey J, Barnes G: Severe illness caused by the products of bacterial metabolism in a child with a short gut. Eur J Pediatr. 1985 May;144(1):63-5. [PubMed:4018104 ]