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Record Information
Version3.6
Creation Date2006-05-22 15:12:35 UTC
Update Date2016-02-11 01:06:04 UTC
HMDB IDHMDB03134
Secondary Accession NumbersNone
Metabolite Identification
Common NameBiocytin
DescriptionBiocytin is a naturally occurring low molecular weight analog of biotin, and a primary source of this essential metabolite for mammals. Biotinidase acts as a hydrolase by cleaving biocytin and biotinyl-peptides, thereby liberating biotin for reutilization. Mammals cannot synthesize biotin and, therefore, derive the vitamin from dietary sources or from the endogenous turnover of the carboxylases. Free biotin can readily enter the biotin pool, whereas holocarboxylases or other biotin-containing proteins must first be degraded proteolytically to biocytin (biotinyl-e-lysine) or biotinyl-peptides. Biocytin is also an especially versatile marker for neuroanatomical investigations, shown that may have multiple applications, especially for labeling neurons. (PMID: 8930409 , 1384763 , 2479450 ).
Structure
Thumb
Synonyms
ValueSource
(3AS-(3aalpha,4beta,6aalpha))-N(6)-(5-(hexahydro-2-oxo-1H-thieno(3,4-D)imidazol-4-yl)-1-oxopentyl)-L-lysineChEBI
Biotinyl-L-lysineChEBI
epsilon-N-Biotinyl-L-lysineChEBI
epsilon-N-BiotinyllysineChEBI
N(epsilon)-Biotinyl-L-lysineChEBI
N-Biotinyl-L-lysineChEBI
N6-D-Biotinyl-L-lysineChEBI
N(6)-D-Biotinyl-L-lysineChEBI
(3AS-(3aalpha,4b,6aalpha))-N(6)-(5-(hexahydro-2-oxo-1H-thieno(3,4-D)imidazol-4-yl)-1-oxopentyl)-L-lysineGenerator
(3AS-(3aalpha,4β,6aalpha))-N(6)-(5-(hexahydro-2-oxo-1H-thieno(3,4-D)imidazol-4-yl)-1-oxopentyl)-L-lysineGenerator
H-Lys(biotinyl)-OHHMDB
N-epsilon-Biotin-L-lysineHMDB
N6-delta-Biotinyl-L-lysineHMDB
Ne-biotynyl-L-lysineHMDB
Chemical FormulaC16H28N4O4S
Average Molecular Weight372.483
Monoisotopic Molecular Weight372.183126094
IUPAC Name(2S)-6-{5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazolidin-4-yl]pentanamido}-2-aminohexanoic acid
Traditional Namebiocytin
CAS Registry Number576-19-2
SMILES
[H][C@]12CS[C@@H](CCCCC(=O)NCCCC[C@H](N)C(O)=O)[C@@]1([H])NC(=O)N2
InChI Identifier
InChI=1S/C16H28N4O4S/c17-10(15(22)23)5-3-4-8-18-13(21)7-2-1-6-12-14-11(9-25-12)19-16(24)20-14/h10-12,14H,1-9,17H2,(H,18,21)(H,22,23)(H2,19,20,24)/t10-,11-,12-,14-/m0/s1
InChI KeyInChIKey=BAQMYDQNMFBZNA-MNXVOIDGSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as biotin and derivatives. These are organic compounds containing a ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBiotin and derivatives
Sub ClassNot Available
Direct ParentBiotin and derivatives
Alternative Parents
Substituents
  • Biotin_derivative
  • L-alpha-amino acid
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Medium-chain fatty acid
  • Thienoimidazolidine
  • Heterocyclic fatty acid
  • Amino fatty acid
  • Fatty acyl
  • Fatty acid
  • N-acyl-amine
  • Imidazolidinone
  • Fatty amide
  • Thiophene
  • Imidazolidine
  • Urea
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Azacycle
  • Dialkylthioether
  • Thioether
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboxylic acid amide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Extracellular
  • Mitochondria
  • Nucleus
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point243 - 246 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.17 mg/mLALOGPS
logP-0.69ALOGPS
logP-2.6ChemAxon
logS-3.3ALOGPS
pKa (Strongest Acidic)2.24ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area133.55 Å2ChemAxon
Rotatable Bond Count11ChemAxon
Refractivity94.66 m3·mol-1ChemAxon
Polarizability40.19 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-00di-0009000000-e021402fd0b719844eb2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-003r-9064000000-5ce2eb2b09d3a1c52ce8View in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-001i-9110000000-d9630fc3192cacdc2fdfView in MoNA
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biofluid LocationsNot Available
Tissue LocationNot Available
Pathways
NameSMPDB LinkKEGG Link
Biotin MetabolismSMP00066map00780
Biotinidase DeficiencySMP00174Not Available
Multiple carboxylase deficiency, neonatal or early onset formSMP00564Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023111
KNApSAcK IDNot Available
Chemspider ID75634
KEGG Compound IDC05552
BioCyc IDNot Available
BiGG ID46012
Wikipedia LinkNot Available
NuGOwiki LinkHMDB03134
Metagene LinkHMDB03134
METLIN IDNot Available
PubChem Compound83814
PDB IDNot Available
ChEBI ID27870
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Spiga S, Fattore L, Puddu MC, Cappai A, Picciau S, Brotzu G, Serra GP, Petruzzo P: Use of biocytin as neuroanatomic tracer in harvested human pancreas: a confocal laser scanning microscopy analysis. Pancreas. 2002 May;24(4):329-35. [11961484 ]
  2. Altemus KL, Lavenex P, Ishizuka N, Amaral DG: Morphological characteristics and electrophysiological properties of CA1 pyramidal neurons in macaque monkeys. Neuroscience. 2005;136(3):741-56. [16344148 ]
  3. Evangelatos SA, Livaniou E, Kakabakos SE, Evangelatos GP, Ithakissios DS: Biotinidase radioassay using an 125I-biotin derivative, avidin, and polyethylene glycol reagents. Anal Biochem. 1991 Aug 1;196(2):385-9. [1776689 ]
  4. Ebrahim H, Dakshinamurti K: Determination of biocytin. Anal Biochem. 1987 May 1;162(2):319-24. [3111297 ]
  5. Suormala TM, Baumgartner ER, Bausch J, Holick W, Wick H: Quantitative determination of biocytin in urine of patients with biotinidase deficiency using high-performance liquid chromatography (HPLC). Clin Chim Acta. 1988 Oct 31;177(3):253-69. [3148376 ]
  6. Hymes J, Fleischhauer K, Wolf B: Biotinylation of biotinidase following incubation with biocytin. Clin Chim Acta. 1995 Jan 16;233(1-2):39-45. [7758201 ]
  7. Baur B, Suormala T, Bernoulli C, Baumgartner ER: Biotin determination by three different methods: specificity and application to urine and plasma ultrafiltrates of patients with and without disorders in biotin metabolism. Int J Vitam Nutr Res. 1998;68(5):300-8. [9789762 ]
  8. van Gog FB, Visser GW, Gowrising RW, Snow GB, van Dongen GA: Synthesis and evaluation of 99mTc/99Tc-MAG3-biotin conjugates for antibody pretargeting strategies. Nucl Med Biol. 1998 Oct;25(7):611-9. [9804042 ]
  9. Hymes J, Wolf B: Biotinidase and its roles in biotin metabolism. Clin Chim Acta. 1996 Nov 15;255(1):1-11. [8930409 ]
  10. McDonald AJ: Neuroanatomical labeling with biocytin: a review. Neuroreport. 1992 Oct;3(10):821-7. [1384763 ]
  11. King MA, Louis PM, Hunter BE, Walker DW: Biocytin: a versatile anterograde neuroanatomical tract-tracing alternative. Brain Res. 1989 Sep 18;497(2):361-7. [2479450 ]

Enzymes

General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Specific function:
Catalytic release of biotin from biocytin, the product of biotin-dependent carboxylases degradation.
Gene Name:
BTD
Uniprot ID:
P43251
Molecular weight:
61132.43
Reactions
Biocytin + Water → Biotin + L-Lysinedetails
General function:
Involved in peptidase activity
Specific function:
Component of the microsomal signal peptidase complex which removes signal peptides from nascent proteins as they are translocated into the lumen of the endoplasmic reticulum
Gene Name:
SPCS1
Uniprot ID:
Q9Y6A9
Molecular weight:
11804.7