D-Dethiobiotin

Identification

Name
D-Dethiobiotin
Accession Number
DB03775  (EXPT01280)
Type
Small Molecule
Groups
Experimental
Description
Not Available
Structure
Thumb
Synonyms
Not Available
Categories
Not Available
UNII
71U5JB52KS
CAS number
Not Available
Weight
Average: 214.2615
Monoisotopic: 214.131742452
Chemical Formula
C10H18N2O3
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
IUPAC Name
6-[(4R,5S)-5-methyl-2-oxoimidazolidin-4-yl]hexanoic acid
SMILES
[H][[email protected]@]1(C)NC(=O)N[[email protected]]1([H])CCCCCC(O)=O

Pharmacology

Indication
Not Available
Structured Indications
Not Available
Pharmacodynamics
Not Available
Mechanism of action
TargetActionsOrganism
UATP-dependent dethiobiotin synthetase BioD 1Not AvailableEscherichia coli (strain K12)
UBiotin synthaseNot AvailableEscherichia coli (strain K12)
UATP-dependent dethiobiotin synthetase BioDNot AvailableMycobacterium tuberculosis
Absorption
Not Available
Volume of distribution
Not Available
Protein binding
Not Available
Metabolism
Not Available
Route of elimination
Not Available
Half life
Not Available
Clearance
Not Available
Toxicity
Not Available
Affected organisms
Not Available
Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
Not Available
Food Interactions
Not Available

References

General References
Not Available
External Links
Human Metabolome Database
HMDB03581
PubChem Compound
445027
PubChem Substance
46504720
ChemSpider
392787
BindingDB
66184
ChEBI
42280
ChEMBL
CHEMBL1232381
HET
DTB
PDB Entries
1dam / 1r30 / 3fpa / 3rdq / 4a0r / 4dne / 5iwk / 5iwp / 5iwr / 5iwt
show 4 more

Clinical Trials

Clinical Trials
Not Available

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
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 RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted ADMET features
PropertyValueProbability
Human Intestinal Absorption+0.5862
Blood Brain Barrier+0.7873
Caco-2 permeable-0.7094
P-glycoprotein substrateSubstrate0.6713
P-glycoprotein inhibitor INon-inhibitor0.9268
P-glycoprotein inhibitor IINon-inhibitor0.9953
Renal organic cation transporterNon-inhibitor0.8833
CYP450 2C9 substrateNon-substrate0.7355
CYP450 2D6 substrateNon-substrate0.8185
CYP450 3A4 substrateNon-substrate0.6697
CYP450 1A2 substrateNon-inhibitor0.935
CYP450 2C9 inhibitorNon-inhibitor0.936
CYP450 2D6 inhibitorNon-inhibitor0.9497
CYP450 2C19 inhibitorNon-inhibitor0.9508
CYP450 3A4 inhibitorNon-inhibitor0.943
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.987
Ames testNon AMES toxic0.8876
CarcinogenicityNon-carcinogens0.9546
BiodegradationNot ready biodegradable0.9602
Rat acute toxicity2.2377 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.8934
hERG inhibition (predictor II)Non-inhibitor0.9386
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
GC-MS Spectrum - GC-MS (3 TMS)GC-MSsplash10-0006-3790100000-c94f58473d108e2927a3
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSNot Available
GC-MS Spectrum - GC-EI-TOFGC-MSsplash10-0006-1690000000-1bda89bfc3811fd0846b
GC-MS Spectrum - GC-MSGC-MSsplash10-0006-3790100000-c94f58473d108e2927a3
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-00kb-0920000000-12242f12c8a3476fe52c
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-014j-1910000000-bca8247f7dffe184f262
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-00kf-9100000000-a1befeec39f013c667cc
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-03di-0490000000-fbb5b60d4417d32465c9
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-0006-9520000000-9247557ea0c296d0d2ad
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-0006-9000000000-a9e635f12ade363f1ca8
LC-MS/MS Spectrum - LC-ESI-qTof , PositiveLC-MS/MSNot Available
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-004i-9200000000-03c3baa9836a6b78a20b
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-004i-9100000000-b90f330888cd6165f177
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-056r-9000000000-7330a6fde54cd5afd3d9
LC-MS/MS Spectrum - LC-ESI-QQ , positiveLC-MS/MSsplash10-0a4i-9000000000-42126ce46ca1e187b36a
LC-MS/MS Spectrum - LC-ESI-IT , positiveLC-MS/MSsplash10-0002-0900000000-2f9eaf52d9aa20dfeb5d
MS/MS Spectrum - , positiveLC-MS/MSsplash10-056s-4910000000-2e5662744c4e67149ef8
1H NMR Spectrum1D NMRNot Applicable
13C NMR Spectrum1D NMRNot Applicable

Taxonomy

Description
This 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 Class
Lipids and lipid-like molecules
Class
Fatty Acyls
Sub Class
Fatty acids and conjugates
Direct Parent
Medium-chain fatty acids
Alternative Parents
Heterocyclic fatty acids / Amino fatty acids / Imidazolidinones / Ureas / Monocarboxylic acids and derivatives / Carboxylic acids / Azacyclic compounds / Organopnictogen compounds / Organonitrogen compounds / Organic oxides
show 2 more
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
show 11 more
Molecular Framework
Aliphatic heteromonocyclic compounds
External Descriptors
dethiobiotin (CHEBI:42280)

Targets

Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Magnesium ion binding
Specific Function
Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can parti...
Gene Name
bioD1
Uniprot ID
P13000
Uniprot Name
ATP-dependent dethiobiotin synthetase BioD 1
Molecular Weight
24139.38 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Iron ion binding
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
Uniprot Name
Biotin synthase
Molecular Weight
38647.785 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]
Kind
Protein
Organism
Mycobacterium tuberculosis
Pharmacological action
Unknown
General Function
Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring.
Specific Function
Atp binding
Gene Name
bioD
Uniprot ID
P9WPQ5
Uniprot Name
ATP-dependent dethiobiotin synthetase BioD
Molecular Weight
22455.665 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235]

Drug created on June 13, 2005 07:24 / Updated on November 09, 2017 03:32