Dethiobiotin (YMDB00075)

Identification
YMDB IDYMDB00075
NameDethiobiotin
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDethiobiotin is an intermediate in biotin biosynthesis from 7-keto-8-aminopelargonate pathway. Biotin is a water soluble, heterocyclic cofactor for a small number of enzymes that facilitate the transfer of CO2 during carboxylation, decarboxylation, and transcarboxylation reactions involved in fatty acid and carbohydrate metabolism. Biotin biosynthesis is found in plants, bacteria, and certain fungi. [Biocyc PWY0-1507]
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • Desthiobiotin
  • (+)-Dethiobiotin
  • (4R,5S)-5-Methyl-2-oxo-4-imidazolidinehexanoic acid
  • (4R-cis)-5-Methyl-2-oxo-4-imidazolidinehexanoic acid
  • D-Dethiobiotin
  • (4R,5S)-5-Methyl-2-oxo-4-imidazolidinehexanoate
  • (4R-cis)-5-Methyl-2-oxo-4-imidazolidinehexanoate
  • Desthiobiotin, (4R-cis)-isomer
  • Desthiobiotin, (cis)-(+-)-isomer
  • 4-Methyl-5-(omega-carboxyamyl)imidazolidone-2
  • 4-Methyl-5-(ω-carboxyamyl)imidazolidone-2
  • 5-Methyl-2-oxo-4-imidazolidinecaproic acid
  • Dethiobiotin
  • epsilon-(4-Methyl-5-imidazolidone-2)caproic acid
  • ε-(4-Methyl-5-imidazolidone-2)caproic acid
CAS number533-48-2
WeightAverage: 214.2615
Monoisotopic: 214.131742452
InChI KeyAUTOLBMXDDTRRT-JGVFFNPUSA-N
InChIInChI=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
IUPAC Name6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid
Traditional IUPAC Name(4R,5S)-dethiobiotin
Chemical FormulaC10H18N2O3
SMILES[H]OC(=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[C@@]1([H])N([H])C(=O)N([H])[C@@]1([H])C([H])([H])[H]
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
StateSolid
Charge0
Melting point157 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Organoleptic PropertiesNot Available
SMPDB Pathways
Biotin BiosynthesisPW002380 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Biotin metabolismec00780 Map00780
SMPDB Reactions
Diaminopimelic acid + Adenosine triphosphate + Carbon dioxide → ADP + phosphate + hydron + Dethiobiotin
Dethiobiotin + S-Adenosyl-L-methionine + Reduced ferredoxin + a sulfurated [sulfur carrier]  → Biotin + L-Methionine + 5'-Deoxyadenosine + an unsulfurated [sulfur carrier] + Oxidized ferredoxin
KEGG Reactions
polysulfur + Dethiobiotin ↔ Biotin + hydron
7,8-diaminononanoic acid + Adenosine triphosphate + Carbon dioxide ↔ Dethiobiotin + phosphate + hydron + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-MS (3 TMS)splash10-0006-3790100000-c94f58473d108e2927a3JSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0006-1690000000-1bda89bfc3811fd0846bJSpectraViewer | MoNA
GC-MSGC-MS Spectrum - GC-MS (Non-derivatized)splash10-0006-3790100000-c94f58473d108e2927a3JSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0002-9500000000-0f385ef69a9d53ba7904JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00ba-9200000000-19b608dc5ef3430fb0b4JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-056s-4910000000-2e5662744c4e67149ef8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9200000000-03c3baa9836a6b78a20bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-004i-9100000000-b90f330888cd6165f177JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-056r-9000000000-7330a6fde54cd5afd3d9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-0a4i-9000000000-42126ce46ca1e187b36aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT , positivesplash10-0002-0900000000-2f9eaf52d9aa20dfeb5dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-056s-4910000000-2e5662744c4e67149ef8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Positivesplash10-0002-0900000000-d8e78a6d347413a0f682JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Positivesplash10-0002-0910000000-b2dd4a92e38e38ef8a7cJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Positivesplash10-066r-9000000000-b2eb519e2e0e5ad91911JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Positivesplash10-002b-4900000000-cf863dd0f0baea9dbe85JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 20V, Negativesplash10-0006-9210000000-a459410fa0babb81e6b9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-178bc9c95d917ad3ea55JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 10V, Negativesplash10-03di-1190000000-d73931a407641bc332caJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - 35V, Negativesplash10-03di-0490000000-ae866fa9d32aecb5a67dJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-0920000000-12242f12c8a3476fe52cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014j-1910000000-bca8247f7dffe184f262JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kf-9100000000-a1befeec39f013c667ccJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-0490000000-fbb5b60d4417d32465c9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9520000000-9247557ea0c296d0d2adJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9000000000-a9e635f12ade363f1ca8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03di-1090000000-7406e098948885bf0fa7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-5930000000-26072ff1fff5e748d959JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9200000000-47fd1748a2d47287944dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-0980000000-f238d4cd8c859f72d3bcJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Muhlenhoff, U., Gerl, M. J., Flauger, B., Pirner, H. M., Balser, S., Richhardt, N., Lill, R., Stolz, J. (2007). "The ISC [corrected] proteins Isa1 and Isa2 are required for the function but not for the de novo synthesis of the Fe/S clusters of biotin synthase in Saccharomyces cerevisiae." Eukaryot Cell 6:495-504.17259550
  • Wu, H., Ito, K., Shimoi, H. (2005). "Identification and characterization of a novel biotin biosynthesis gene in Saccharomyces cerevisiae." Appl Environ Microbiol 71:6845-6855.16269718
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.
External Links:
ResourceLink
CHEBI ID42280
HMDB IDHMDB03581
Pubchem Compound ID643
Kegg IDC01909
ChemSpider ID24785644
FOODB IDFDB023201
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Biotin synthase, mitochondrial
General function:
Involved in catalytic activity
Specific function:
Dethiobiotin + sulfur + 2 S-adenosyl-L- methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine
Gene Name:
BIO2
Uniprot ID:
P32451
Molecular weight:
41883.80078
Reactions
Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine → biotin + 2 L-methionine + 2 5'-deoxyadenosine.
Protein Details
2. Dethiobiotin synthetase
General function:
Involved in magnesium ion binding
Specific function:
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Gene Name:
BIO4
Uniprot ID:
P53630
Molecular weight:
26256.69922
Reactions
ATP + 7,8-diaminononanoate + CO(2) → ADP + phosphate + dethiobiotin.