Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:18:55 UTC
HMDB IDHMDB0000410
Secondary Accession Numbers
  • HMDB00410
Metabolite Identification
Common Name3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid
Description3-Hydroxy-2-methyl-butanoic acid (HMBA) is a normal urinary metabolite involved in the isoleucine catabolism, as well as presumably b-oxidation of fatty acids and ketogenesis, excreted in abnormally high amounts in beta-ketothiolase deficiency. Differences in the enantiomeric ratio of HMBA may originate from the enantioselectivity of different enzyme systems (PMID 10755375 ).
Structure
Data?1582752129
Synonyms
ValueSource
3-Hydroxy-2-methyl-[S-(R,R)]-butanoateGenerator
3-Hydroxy-2-methyl-[S-(r*,r*)]-butanoateHMDB
3-Hydroxy-2-methyl-[S-(r*,r*)]-butanoic acidHMDB
[S-(R,R)]-3-Hydroxy-2-methyl-butanoateHMDB
[S-(R,R)]-3-Hydroxy-2-methyl-butanoic acidHMDB
Chemical FormulaC5H10O3
Average Molecular Weight118.1311
Monoisotopic Molecular Weight118.062994186
IUPAC Name(2R,3R)-3-hydroxy-2-methylbutanoic acid
Traditional Name(2R,3R)-3-hydroxy-2-methylbutanoic acid
CAS Registry Number84567-98-6
SMILES
C[C@@H](O)[C@@H](C)C(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-3(4(2)6)5(7)8/h3-4,6H,1-2H3,(H,7,8)/t3-,4-/m1/s1
InChI KeyVEXDRERIMPLZLU-QWWZWVQMSA-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
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Methyl-branched fatty acid
  • Hydroxy acid
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Physical Properties
StateSolid
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
Water Solubility336 g/LALOGPS
logP-0.13ALOGPS
logP0.16ChemAxon
logS0.45ALOGPS
pKa (Strongest Acidic)4.51ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity28.04 m³·mol⁻¹ChemAxon
Polarizability11.8 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+125.65231661259
DarkChem[M-H]-122.531661259
AllCCS[M+H]+129.86532859911
AllCCS[M-H]-125.83332859911
DeepCCS[M+H]+127.17530932474
DeepCCS[M-H]-123.58330932474
DeepCCS[M-2H]-160.74230932474
DeepCCS[M+Na]+136.25830932474
AllCCS[M+H]+129.932859911
AllCCS[M+H-H2O]+125.732859911
AllCCS[M+NH4]+133.732859911
AllCCS[M+Na]+134.932859911
AllCCS[M-H]-125.832859911
AllCCS[M+Na-2H]-129.232859911
AllCCS[M+HCOO]-132.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acidC[C@@H](O)[C@@H](C)C(O)=O2083.5Standard polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acidC[C@@H](O)[C@@H](C)C(O)=O1019.9Standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acidC[C@@H](O)[C@@H](C)C(O)=O1040.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,1TMS,isomer #1C[C@@H](O[Si](C)(C)C)[C@@H](C)C(=O)O1128.6Semi standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,1TMS,isomer #2C[C@@H](O)[C@@H](C)C(=O)O[Si](C)(C)C1061.3Semi standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,2TMS,isomer #1C[C@@H](O[Si](C)(C)C)[C@@H](C)C(=O)O[Si](C)(C)C1206.7Semi standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,1TBDMS,isomer #1C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)C(=O)O1367.1Semi standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,1TBDMS,isomer #2C[C@@H](O)[C@@H](C)C(=O)O[Si](C)(C)C(C)(C)C1283.7Semi standard non polar33892256
3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid,2TBDMS,isomer #1C[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](C)C(=O)O[Si](C)(C)C(C)(C)C1646.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-0097-9100000000-4296c67313a78a0150742017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (2 TMS) - 70eV, Positivesplash10-00ds-9610000000-ea139d8674dafe6ab92a2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 10V, Positive-QTOFsplash10-0uxr-3900000000-d8f24d02712f429591a72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 20V, Positive-QTOFsplash10-0zgi-9800000000-0821ba5748054e7de3692017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 40V, Positive-QTOFsplash10-0a4i-9000000000-e5b2f743cb4dd5e99ec52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 10V, Negative-QTOFsplash10-014i-5900000000-587bb9b1fdf10856b3a12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 20V, Negative-QTOFsplash10-05fr-9100000000-a33491d8a46967cdd2d32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 40V, Negative-QTOFsplash10-0a4i-9000000000-1ec2b5bb3af9f3c925ca2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 10V, Negative-QTOFsplash10-01b9-8900000000-6e362f577b3d827a83872021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 20V, Negative-QTOFsplash10-05fr-9100000000-6950ab2628a11bf6839a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 40V, Negative-QTOFsplash10-052f-9000000000-5278bf25a974c9f303692021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 10V, Positive-QTOFsplash10-0zgi-9400000000-aee3a280a6df1ae985b62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 20V, Positive-QTOFsplash10-0002-9000000000-45e4e2c8c6ea7216859f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Hydroxy-2-methyl-[S-(R,R)]-butanoic acid 40V, Positive-QTOFsplash10-052b-9000000000-845222220a578798d8ce2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022026
KNApSAcK IDNot Available
Chemspider ID13628080
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5399
PubChem Compound12313369
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKikukawa, Tadashi; Imaida, Motomasa; Tai, Akira. Synthesis of the sex-attractant of pine sawflies (diprion species); (2S,3R,7R)- and (2S,3R,7S)-3,7-dimethylpentadecan-2-ol. Chemistry Letters (1982), (11), 1799-802.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Herrmann W, Schorr H, Bodis M, Knapp JP, Muller A, Stein G, Geisel J: Role of homocysteine, cystathionine and methylmalonic acid measurement for diagnosis of vitamin deficiency in high-aged subjects. Eur J Clin Invest. 2000 Dec;30(12):1083-9. [PubMed:11122323 ]
  2. Heil M, Podebrad F, Prado E, Beck T, Mosand A, Sewell AC, Bohles H, Lehnert W: Enantioselective analysis of ketone bodies in patients with beta-ketothiolase deficiency, medium-chain acyl coenzyme A dehydrogenase deficiency and ketonemic vomiting. J Chromatogr B Biomed Sci Appl. 2000 Mar 10;739(2):313-24. [PubMed:10755375 ]