Dethiobiotin (PAMDB000517)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000517
Identification
Name: Dethiobiotin
Description:Dethiobiotin 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
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Desthiobiotin
  • DTB
Chemical Formula: C10H18N2O3
Average Molecular Weight: 214.2615
Monoisotopic Molecular Weight: 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
Taxonomy DescriptionThis compound 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.
Kingdom Organic compounds
Super ClassLipids and lipid-like molecules
Class Fatty Acyls
Sub ClassFatty acids and conjugates
Direct Parent Medium-chain fatty acids
Alternative Parents
Substituents
  • Medium-chain fatty acid
  • Heterocyclic fatty acid
  • Amino fatty acid
  • Imidazolidinone
  • Imidazolidine
  • Urea
  • Azacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-1
Melting point: 157 °C
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility1.27 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity54.4 m3·mol-1ChemAxon
Polarizability23.15 Å3ChemAxon
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
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
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
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0006-3790100000-c94f58473d108e2927a3View in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
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
1D NMR1H NMR SpectrumNot Available
1D NMR13C NMR SpectrumNot Available
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