Record Information
Version2.0
Creation Date2012-05-31 13:59:58 -0600
Update Date2015-09-13 12:56:13 -0600
Secondary Accession Numbers
  • ECMDB03581
Identification
Name:Dethiobiotin
DescriptionDethiobiotin is a synthetic metabolite that mimic the effects of biotin on gene expression and thus have biotin-like activities. It is an intermediate in biotin metabolism, and converted to biotin via biotin synthase (EC:2.8.1.6). (KEGG) Biotin serves as a coenzyme for carboxylases such as propionyl-CoA carboxylase. (PMID 12730407)
Structure
Thumb
Synonyms:
  • Desthiobiotin
  • DTB
Chemical Formula:C10H18N2O3
Weight:Average: 214.2615
Monoisotopic: 214.131742452
InChI Key:AUTOLBMXDDTRRT-JGVFFNPUSA-N
InChI: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
CAS number:533-48-2
IUPAC Name:6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid
Traditional IUPAC Name:(4R,5S)-dethiobiotin
SMILES:[H][C@@]1(C)NC(=O)N[C@]1([H])CCCCCC(O)=O
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
Physical Properties
State:Solid
Charge:-1
Melting point:157 °C
Experimental Properties:
PropertyValueSource
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
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
[2Fe-2S] iron-sulfur cluster + S-Adenosylmethionine + Dethiobiotin > [2Fe-1S] desulfurated iron-sulfur cluster + Biotin + 5'-Deoxyadenosine + Hydrogen ion + L-Methionine
Adenosine triphosphate + Carbon dioxide + 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate
Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Adenosine triphosphate + 7,8-Diaminononanoate + Carbon dioxide <> ADP + Phosphate + Dethiobiotin
<i>S</i>-sulfanyl-[acceptor] + Dethiobiotin + S-Adenosylmethionine > an unsulfurated sulfur acceptor + Biotin + 5'-Deoxyadenosine + L-Methionine + Hydrogen ion
Carbon dioxide + 7,8-Diaminononanoate + Adenosine triphosphate > Hydrogen ion + Dethiobiotin + Phosphate + ADP
Dethiobiotin + Hydrogen sulfide + 2 S-adenosyl-L-methionine > Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Adenosine triphosphate + 7,8-Diaminononanoate + Carbon dioxide > ADP + Inorganic phosphate + Dethiobiotin
7,8-Diaminononanoate + Adenosine triphosphate + Carbon dioxide + 7,8-Diaminononanoate > Dethiobiotin + Adenosine diphosphate + Phosphate + ADP
Dethiobiotin + 2 S-adenosyl-L-methionine + 2 Hydrogen ion + a sulfurated [sulfur carrier] > Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Adenosine triphosphate + Carbon dioxide + 7 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate
Dethiobiotin + Sulfur donor + 2 S-Adenosylmethionine + 2 e- + 2 Hydrogen ion <> Biotin +2 L-Methionine +2 5'-Deoxyadenosine
Adenosine triphosphate + Carbon dioxide + 7 7,8-Diaminononanoate <> ADP + Dethiobiotin +3 Hydrogen ion + Phosphate
SMPDB Pathways:
Biotin metabolismPW000762 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:
  • biotin biosynthesis from 7-keto-8-aminopelargonate PWY0-1507
Concentrations
Not Available
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 SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Rodriguez-Melendez, R., Lewis, B., McMahon, R. J., Zempleni, J. (2003). "Diaminobiotin and desthiobiotin have biotin-like activities in Jurkat cells." J Nutr 133:1259-1264. Pubmed: 12730407
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Kuzuhara, 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)
External Links:
ResourceLink
CHEBI ID16691
HMDB IDHMDB03581
Pubchem Compound ID643
Kegg IDC01909
ChemSpider ID392787
Wikipedia IDNot Available
BioCyc IDDETHIOBIOTIN
EcoCyc IDDETHIOBIOTIN
Ligand ExpoDTB

Enzymes

General function:
Involved in magnesium ion binding
Specific function:
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Gene Name:
ynfK
Uniprot ID:
P0A6E9
Molecular weight:
24981
Reactions
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin.
General function:
Involved in catalytic activity
Specific function:
Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
Gene Name:
bioB
Uniprot ID:
P12996
Molecular weight:
38648
Reactions
Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine.
General function:
Involved in magnesium ion binding
Specific function:
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Gene Name:
bioD
Uniprot ID:
P13000
Molecular weight:
24139
Reactions
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin.