Showing metabocard for Dethiobiotin (BMDB0003581)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-09-30 23:05:27 UTC
Update Date2020-04-22 15:12:33 UTC
BMDB IDBMDB0003581
Secondary Accession Numbers
  • BMDB03581
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. Based on a literature review a significant number of articles have been published on Dethiobiotin.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
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)-isomerMeSH
Desthiobiotin, (cis)-(+-)-isomerMeSH
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
[H][C@@]1(C)NC(=O)N[C@]1([H])CCCCCC(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
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Adiposome
  • Cell membrane
  • Cytoplasm
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point157 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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 RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0006-3790100000-c94f58473d108e2927a3View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-1690000000-1bda89bfc3811fd0846bView in MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0006-3790100000-c94f58473d108e2927a3View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-0f385ef69a9d53ba7904View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00ba-9200000000-19b608dc5ef3430fb0b4View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-056s-4910000000-2e5662744c4e67149ef8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9200000000-03c3baa9836a6b78a20bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9100000000-b90f330888cd6165f177View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-056r-9000000000-7330a6fde54cd5afd3d9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a4i-9000000000-42126ce46ca1e187b36aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-0002-0900000000-2f9eaf52d9aa20dfeb5dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-056s-4910000000-2e5662744c4e67149ef8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0002-0900000000-d8e78a6d347413a0f682View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-0910000000-b2dd4a92e38e38ef8a7cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-066r-9000000000-b2eb519e2e0e5ad91911View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-002b-4900000000-cf863dd0f0baea9dbe85View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-a459410fa0babb81e6b9View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-178bc9c95d917ad3ea55View in MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03di-1190000000-d73931a407641bc332caView in MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-03di-0490000000-ae866fa9d32aecb5a67dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-0920000000-12242f12c8a3476fe52cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014j-1910000000-bca8247f7dffe184f262View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kf-9100000000-a1befeec39f013c667ccView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0490000000-fbb5b60d4417d32465c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9520000000-9247557ea0c296d0d2adView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-a9e635f12ade363f1ca8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-1090000000-7406e098948885bf0fa7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-5930000000-26072ff1fff5e748d959View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-47fd1748a2d47287944dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-0980000000-f238d4cd8c859f72d3bcView in MoNA
1D NMR1H NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, D2O, experimental)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Adiposome
  • Cell membrane
  • Cytoplasm
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0003581
DrugBank IDDB03775
Phenol Explorer Compound IDNot Available
FooDB IDFDB023201
KNApSAcK IDC00000757
Chemspider ID392787
KEGG Compound IDC01909
BioCyc IDDETHIOBIOTIN
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID3351
PubChem Compound445027
PDB IDNot Available
ChEBI ID42280
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)Not Available
General ReferencesNot Available