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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-13 00:50:12 UTC
Update Date2021-09-14 15:41:33 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. Based on a literature review a significant number of articles have been published on Dethiobiotin.
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)-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
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

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point157 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+MetCCS_train_pos144.13630932474
[M+H]+Not Available144.26http://allccs.zhulab.cn/database/detail?ID=AllCCS00000453
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.27 g/LALOGPS
logP10(0.72) g/LALOGPS
logP10(0.73) g/LChemAxon
logS10(-2.2) g/LALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+149.7431661259
DarkChem[M-H]-148.89631661259
DeepCCS[M+H]+149.55430932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DethiobiotinC[C@@H]1NC(=O)N[C@@H]1CCCCCC(O)=O3090.6Standard polar33892256
DethiobiotinC[C@@H]1NC(=O)N[C@@H]1CCCCCC(O)=O2092.9Standard non polar33892256
DethiobiotinC[C@@H]1NC(=O)N[C@@H]1CCCCCC(O)=O2204.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Dethiobiotin,1TMS,isomer #1C[C@@H]1NC(=O)N[C@@H]1CCCCCC(=O)O[Si](C)(C)C2116.6Semi standard non polar33892256
Dethiobiotin,1TMS,isomer #2C[C@H]1[C@@H](CCCCCC(=O)O)NC(=O)N1[Si](C)(C)C2111.1Semi standard non polar33892256
Dethiobiotin,1TMS,isomer #3C[C@@H]1NC(=O)N([Si](C)(C)C)[C@@H]1CCCCCC(=O)O2106.2Semi standard non polar33892256
Dethiobiotin,2TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)NC(=O)N1[Si](C)(C)C2157.1Semi standard non polar33892256
Dethiobiotin,2TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)NC(=O)N1[Si](C)(C)C2130.6Standard non polar33892256
Dethiobiotin,2TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)NC(=O)N1[Si](C)(C)C3519.8Standard polar33892256
Dethiobiotin,2TMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C2155.3Semi standard non polar33892256
Dethiobiotin,2TMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C2129.6Standard non polar33892256
Dethiobiotin,2TMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C3517.4Standard polar33892256
Dethiobiotin,2TMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2002.2Semi standard non polar33892256
Dethiobiotin,2TMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2085.1Standard non polar33892256
Dethiobiotin,2TMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2685.8Standard polar33892256
Dethiobiotin,3TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2002.5Semi standard non polar33892256
Dethiobiotin,3TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2134.2Standard non polar33892256
Dethiobiotin,3TMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C)N([Si](C)(C)C)C(=O)N1[Si](C)(C)C2434.7Standard polar33892256
Dethiobiotin,1TBDMS,isomer #1C[C@@H]1NC(=O)N[C@@H]1CCCCCC(=O)O[Si](C)(C)C(C)(C)C2348.6Semi standard non polar33892256
Dethiobiotin,1TBDMS,isomer #2C[C@H]1[C@@H](CCCCCC(=O)O)NC(=O)N1[Si](C)(C)C(C)(C)C2349.6Semi standard non polar33892256
Dethiobiotin,1TBDMS,isomer #3C[C@@H]1NC(=O)N([Si](C)(C)C(C)(C)C)[C@@H]1CCCCCC(=O)O2350.4Semi standard non polar33892256
Dethiobiotin,2TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)NC(=O)N1[Si](C)(C)C(C)(C)C2611.8Semi standard non polar33892256
Dethiobiotin,2TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)NC(=O)N1[Si](C)(C)C(C)(C)C2543.9Standard non polar33892256
Dethiobiotin,2TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)NC(=O)N1[Si](C)(C)C(C)(C)C3337.9Standard polar33892256
Dethiobiotin,2TBDMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C(C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C(C)(C)C2601.6Semi standard non polar33892256
Dethiobiotin,2TBDMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C(C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C(C)(C)C2538.6Standard non polar33892256
Dethiobiotin,2TBDMS,isomer #2C[C@@H]1NC(=O)N([Si](C)(C)C(C)(C)C)[C@@H]1CCCCCC(=O)O[Si](C)(C)C(C)(C)C3312.4Standard polar33892256
Dethiobiotin,2TBDMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2427.4Semi standard non polar33892256
Dethiobiotin,2TBDMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2562.9Standard non polar33892256
Dethiobiotin,2TBDMS,isomer #3C[C@H]1[C@@H](CCCCCC(=O)O)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2714.1Standard polar33892256
Dethiobiotin,3TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2647.9Semi standard non polar33892256
Dethiobiotin,3TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2762.6Standard non polar33892256
Dethiobiotin,3TBDMS,isomer #1C[C@H]1[C@@H](CCCCCC(=O)O[Si](C)(C)C(C)(C)C)N([Si](C)(C)C(C)(C)C)C(=O)N1[Si](C)(C)C(C)(C)C2669.0Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental GC-MSGC-MS Spectrum - Dethiobiotin GC-MS (3 TMS)splash10-0006-3790100000-c94f58473d108e2927a32014-06-16HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dethiobiotin GC-EI-TOF (Non-derivatized)splash10-0006-1690000000-1bda89bfc3811fd0846b2017-09-12HMDB team, MONA, MassBankView Spectrum
Experimental GC-MSGC-MS Spectrum - Dethiobiotin GC-MS (Non-derivatized)splash10-0006-3790100000-c94f58473d108e2927a32017-09-12HMDB team, MONA, MassBankView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dethiobiotin GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-0f385ef69a9d53ba79042016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dethiobiotin GC-MS (1 TMS) - 70eV, Positivesplash10-00ba-9200000000-19b608dc5ef3430fb0b42017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dethiobiotin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dethiobiotin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-qTof , Positive-QTOFsplash10-056s-4910000000-2e5662744c4e67149ef82017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-QQ , positive-QTOFsplash10-004i-9200000000-03c3baa9836a6b78a20b2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-QQ , positive-QTOFsplash10-004i-9100000000-b90f330888cd6165f1772017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-QQ , positive-QTOFsplash10-056r-9000000000-7330a6fde54cd5afd3d92017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-QQ , positive-QTOFsplash10-0a4i-9000000000-42126ce46ca1e187b36a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin LC-ESI-IT , positive-QTOFsplash10-0002-0900000000-2f9eaf52d9aa20dfeb5d2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin , positive-QTOFsplash10-056s-4910000000-2e5662744c4e67149ef82017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 35V, Positive-QTOFsplash10-0002-0900000000-d8e78a6d347413a0f6822021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 10V, Positive-QTOFsplash10-0002-0910000000-b2dd4a92e38e38ef8a7c2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 40V, Positive-QTOFsplash10-066r-9000000000-b2eb519e2e0e5ad919112021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 20V, Positive-QTOFsplash10-002b-4900000000-cf863dd0f0baea9dbe852021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 20V, Negative-QTOFsplash10-0006-9210000000-a459410fa0babb81e6b92021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 40V, Negative-QTOFsplash10-0006-9000000000-178bc9c95d917ad3ea552021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 10V, Negative-QTOFsplash10-03di-1190000000-d73931a407641bc332ca2021-09-20HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Dethiobiotin 35V, Negative-QTOFsplash10-03di-0490000000-ae866fa9d32aecb5a67d2021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 10V, Positive-QTOFsplash10-00kb-0920000000-12242f12c8a3476fe52c2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 20V, Positive-QTOFsplash10-014j-1910000000-bca8247f7dffe184f2622015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 40V, Positive-QTOFsplash10-00kf-9100000000-a1befeec39f013c667cc2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 10V, Negative-QTOFsplash10-03di-0490000000-fbb5b60d4417d32465c92015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 20V, Negative-QTOFsplash10-0006-9520000000-9247557ea0c296d0d2ad2015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 40V, Negative-QTOFsplash10-0006-9000000000-a9e635f12ade363f1ca82015-09-15Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 10V, Negative-QTOFsplash10-03di-1090000000-7406e098948885bf0fa72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 20V, Negative-QTOFsplash10-01ox-5930000000-26072ff1fff5e748d9592021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 40V, Negative-QTOFsplash10-0006-9200000000-47fd1748a2d47287944d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dethiobiotin 10V, Positive-QTOFsplash10-014j-0980000000-f238d4cd8c859f72d3bc2021-09-23Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
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 IDC00000757
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 IDNot Available
Good Scents IDNot Available
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 ]