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Record Information
StatusExpected but not Quantified
Creation Date2006-05-22 15:12:35 UTC
Update Date2017-12-07 01:50:32 UTC
Secondary Accession Numbers
  • HMDB03134
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 ).
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
InChI Identifier
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic acids and derivatives
Sub ClassCarboxylic acids and derivatives
Direct ParentL-alpha-amino acids
Alternative Parents
  • L-alpha-amino acid
  • Imidazolyl carboxylic acid derivative
  • Medium-chain fatty acid
  • Heterocyclic fatty acid
  • Fatty acid
  • Fatty acyl
  • Thiolane
  • 2-imidazoline
  • Amino acid
  • Isourea
  • Azacycle
  • Carboximidic acid
  • Carboximidic acid derivative
  • Organoheterocyclic compound
  • Dialkylthioether
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Carboxylic acid
  • Thioether
  • Monocarboxylic acid or derivatives
  • Organic oxide
  • Organonitrogen compound
  • Primary aliphatic amine
  • Organooxygen compound
  • Organic oxygen compound
  • Primary amine
  • Organic nitrogen compound
  • Organopnictogen compound
  • Amine
  • Carbonyl group
  • Hydrocarbon derivative
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors

Biological Location:


  Cell and elements:



Naturally occurring process:

  Biological process:

    Biochemical pathway:

Physical Properties
Experimental Properties
Melting Point243 - 246 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility0.17 g/LALOGPS
pKa (Strongest Acidic)2.24ChemAxon
pKa (Strongest Basic)9.53ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area133.55 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity94.66 m³·mol⁻¹ChemAxon
Polarizability40.19 ųChemAxon
Number of Rings2ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0035-9633000000-af428e64c7164519343bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9745000000-c60f47e829fe15e1e793View in MoNA
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
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-05di-0429000000-0bfe49385b5205b2e046View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0fc1-3922000000-9e29cfc78fb1faa6e51bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001j-9500000000-e9574b5d68137a62b679View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0009000000-105dd5c3f301cc7dc40eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0006-9437000000-8ea9d972c1d5eeb423e9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-9300000000-6a46fba2d13aba09d4f0View in MoNA
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Extracellular
  • Mitochondria
  • Nucleus
Biofluid LocationsNot Available
Tissue LocationNot Available
Biotin MetabolismPw000013Pw000013 greyscalePw000013 simpleMap00780
Biotinidase DeficiencyPw000092Pw000092 greyscalePw000092 simpleNot Available
Multiple carboxylase deficiency, neonatal or early onset formPw000540Pw000540 greyscalePw000540 simpleNot 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
METLIN IDNot Available
PubChem Compound83814
PDB IDNot Available
ChEBI ID27870
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. [PubMed: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. [PubMed: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. [PubMed:1776689 ]
  4. Ebrahim H, Dakshinamurti K: Determination of biocytin. Anal Biochem. 1987 May 1;162(2):319-24. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed: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. [PubMed:9804042 ]
  9. Hymes J, Wolf B: Biotinidase and its roles in biotin metabolism. Clin Chim Acta. 1996 Nov 15;255(1):1-11. [PubMed:8930409 ]
  10. McDonald AJ: Neuroanatomical labeling with biocytin: a review. Neuroreport. 1992 Oct;3(10):821-7. [PubMed: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. [PubMed:2479450 ]


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:
Uniprot ID:
Molecular weight:
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:
Uniprot ID:
Molecular weight: