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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2006-08-13 00:50:12 UTC
Update Date2020-06-24 21:49:52 UTC
HMDB IDHMDB0003581
Secondary Accession Numbers
  • HMDB03581
Metabolite Identification
Common NameDethiobiotin
DescriptionDethiobiotin belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. Dethiobiotin is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1593035392
Synonyms
ValueSource
(+)-DethiobiotinChEBI
(4R,5S)-5-Methyl-2-oxo-4-imidazolidinehexanoic acidChEBI
(4R-cis)-5-Methyl-2-oxo-4-imidazolidinehexanoic acidChEBI
D-DethiobiotinChEBI
DesthiobiotinChEBI
(4R,5S)-5-Methyl-2-oxo-4-imidazolidinehexanoateGenerator
(4R-cis)-5-Methyl-2-oxo-4-imidazolidinehexanoateGenerator
Desthiobiotin, (4R-cis)-isomerHMDB
Desthiobiotin, (cis)-(+-)-isomerHMDB
4-Methyl-5-(omega-carboxyamyl)imidazolidone-2HMDB
4-Methyl-5-(ω-carboxyamyl)imidazolidone-2HMDB
5-Methyl-2-oxo-4-imidazolidinecaproic acidHMDB
DethiobiotinHMDB
epsilon-(4-Methyl-5-imidazolidone-2)caproic acidHMDB
ε-(4-Methyl-5-imidazolidone-2)caproic acidHMDB
Chemical FormulaC10H18N2O3
Average Molecular Weight214.2615
Monoisotopic Molecular Weight214.131742452
IUPAC Name6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid
Traditional Name(4R,5S)-dethiobiotin
CAS Registry Number533-48-2
SMILES
C[C@@H]1NC(=O)N[C@@H]1CCCCCC(O)=O
InChI Identifier
InChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)/t7-,8+/m0/s1
InChI KeyAUTOLBMXDDTRRT-JGVFFNPUSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentMedium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Amino fatty acid
  • Heterocyclic fatty acid
  • Imidazolidinone
  • Imidazolidine
  • Carbonic acid derivative
  • Urea
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Carbonyl group
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Biological role:

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point157 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility1.27 g/LALOGPS
logP0.72ALOGPS
logP0.73ChemAxon
logS-2.2ALOGPS
pKa (Strongest Acidic)4.63ChemAxon
pKa (Strongest Basic)-1.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area78.43 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity54.4 m³·mol⁻¹ChemAxon
Polarizability23.15 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0006-3790100000-c94f58473d108e2927a3Spectrum
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-1690000000-1bda89bfc3811fd0846bSpectrum
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0006-3790100000-c94f58473d108e2927a3Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-0f385ef69a9d53ba7904Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00ba-9200000000-19b608dc5ef3430fb0b4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-056s-4910000000-2e5662744c4e67149ef8Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9200000000-03c3baa9836a6b78a20bSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9100000000-b90f330888cd6165f177Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-056r-9000000000-7330a6fde54cd5afd3d9Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a4i-9000000000-42126ce46ca1e187b36aSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-0002-0900000000-2f9eaf52d9aa20dfeb5dSpectrum
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-056s-4910000000-2e5662744c4e67149ef8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-0920000000-12242f12c8a3476fe52cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014j-1910000000-bca8247f7dffe184f262Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kf-9100000000-a1befeec39f013c667ccSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0490000000-fbb5b60d4417d32465c9Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9520000000-9247557ea0c296d0d2adSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-a9e635f12ade363f1ca8Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
1D NMR13C NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDDB03775
Phenol Explorer Compound IDNot Available
FooDB IDFDB023201
KNApSAcK IDNot Available
Chemspider ID392787
KEGG Compound IDC01909
BioCyc IDDETHIOBIOTIN
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3351
PubChem Compound445027
PDB IDNot Available
ChEBI ID42280
Food Biomarker OntologyNot Available
VMH IDDTBT
MarkerDB ID
References
Synthesis ReferenceKuzuhara, Hiroyoshi; Ohrui, Hiroshi; Emoto, Sakae. Syntheses with azido sugars. II. Conversion of D-glucose to (+)-dethiobiotin. Agricultural and Biological Chemistry (1971), 35(1), 8-17.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Rodriguez-Melendez R, Lewis B, McMahon RJ, Zempleni J: Diaminobiotin and desthiobiotin have biotin-like activities in Jurkat cells. J Nutr. 2003 May;133(5):1259-64. [PubMed:12730407 ]