5-(Biotinamido)pentylamine

Name: 5-(Biotinamido)pentylamine
Brand: BOC Sciences
Rating: 5 (1 reviews)

CAS No.: 115416-38-1

Cat No.: BP-500153

Purity: 95% 4.5

5-(Biotinamido)pentylamine is a biotin-containing linker featuring a biotinamide headgroup connected through a flexible pentyl chain to a terminal primary amine. Structurally, it provides a convenient handle for amide coupling or reductive amination to attach to PROTAC scaffolds, while the biotin moiety enables high-affinity association with streptavidin or avidin systems used to position, capture, or immobilize protein-binding components. In targeted protein degradation workflows, such biotinylated linkers are commonly employed to facilitate modular conjugation strategies, for example by tethering ligands or recruiting protein-binding partners to a defined surface or scaffold, thereby improving effective local concentration and experimental manipulability during ternary-complex formation studies. The terminal amine supports routine derivatization for building degraders, including attachment to carboxyl-activated warheads or spacer arms, making this reagent valuable for linker optimization, mechanistic assays, and biotin-based affinity purification of PROTAC intermediates.

Structure of 115416-38-1

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Category

PROTAC Linker

Molecular Formula

C15H28N4O2S

Molecular Weight

328.47

Appearance

Light Brown Solid

* For research and manufacturing use only. Not for human or clinical use.

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Purity

95%

Solubility

In DMSO: 100 mg/mL (304.44 mM; Need ultrasonic)

Appearance

Light Brown Solid

Application

Reagent used in the preparation of a variety of biotin derivatives.

Storage

Powder, -20°C, 3 years; In solvent, -80°C, 6 months; -20°C, 1 month

Shipping

Room temperature in continental US; may vary elsewhere.

IUPACName

5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]-N-(5-aminopentyl)pentanamide

Synonyms

(3aS,4S,6aR)-N-(5-Aminopentyl)hexahydro-2-oxo-thieno[3,4-d]imidazole-4-pentanamide; Biotinyl Cadaverine; Cadaverine-X-biotin; N-(5-Aminopentyl)biotinamide;

Boiling Point

652°C at 760mmHg

Density

1.131g/cm3

InChI Key

CCSGGWGTGOLEHK-OBJOEFQTSA-N

InChI

InChI=1S/C15H28N4O2S/c16-8-4-1-5-9-17-13(20)7-3-2-6-12-14-11(10-22-12)18-15(21)19-14/h11-12,14H,1-10,16H2,(H,17,20)(H2,18,19,21)/t11-,12-,14-/m0/s1

SMILES

C1C2C(C(S1)CCCCC(=O)NCCCCCN)NC(=O)N2

1. Identification of new amine acceptor protein substrate candidates of transglutaminase in rat liver extract: use of 5-(biotinamido) pentylamine as a probe

Akira Ichikawa, Jin Ishizaki, Manabu Morita, Kentaro Tanaka, Koji Ikura Biosci Biotechnol Biochem. 2008 Apr;72(4):1056-62.doi: 10.1271/bbb.70796.Epub 2008 Apr 7.

Transglutaminases (TGs) are a family of enzymes that catalyze Ca(2+)-dependent post-translational modification of proteins by introducing protein-protein crosslinks (between specific glutamine and lysine residues), amine incorporation, and site-specific deamidation. In this study, new amine acceptor protein substrates of TG were isolated from rat liver extract and identified using 5-(biotinamido) pentylamine, a biotinylated primary amine substrate, as a probe. TG protein substrate candidates labeled with biotin by endogenous TG activity were isolated and recovered by avidin column chromatography. Proteins with molecular masses of 40, 42, and 45 kDa were the main components of the labeled proteins. Determination of their partial amino acid sequences and immunoblotting analyses were done to identify them. The 45-kDa protein was identical with betaine-homocysteine S-methyltransferase (EC 2.2.2.5), which was identified in our previous study. The 40- and 42-kDa proteins were identified as arginase-I (EC 3.5.3.1) and fructose-1,6-bisphosphatase (EC 3.1.3.11) respectively. TG catalyzed incorporation of 5-(biotinamido) pentylamine into both arginase-I and fructose-1,6-bisphosphatase purified from rat liver was confirmed in vitro. These results suggest that these two enzymes are the new protein substrate candidates of TG and that they can be modified post-translationally by cellular TG.

2. Identification of transglutaminase substrates in HT29 colon cancer cells: use of 5-(biotinamido)pentylamine as a transglutaminase-specific probe

K N Lee, M D Maxwell, M K Patterson Jr, P J Birckbichler, E Conway Biochim Biophys Acta. 1992 Jul 22;1136(1):12-6.doi: 10.1016/0167-4889(92)90078-p.

A biotinamine probe, 5-(biotinamido)pentylamine, was used for biotin-labeling of proteins in HT29 colon cancer cell extracts by endogenous transglutaminase activity. The biotin-labeled protein substrates were isolated and recovered by avidin-affinity chromatography. The proteins were separated using SDS-polyacrylamide gel electrophoresis, electroblotted onto a polyvinylidene difluoride membrane, visualized using Coomassie blue, cut out, and sequenced. Amino acid sequence data identified human fructose-1,6-bisphosphate aldolase A, an intracellular protein, as a substrate for cellular transglutaminase.

3. A microtiter plate transglutaminase assay utilizing 5-(biotinamido)pentylamine as substrate

T F Slaughter, K E Achyuthan, T S Lai, C S Greenberg Anal Biochem. 1992 Aug 15;205(1):166-71.doi: 10.1016/0003-2697(92)90594-w.

Transglutaminases belong to an important family of enzymes involved in hemostasis, skin formation, and wound healing. We describe a technique for the measurement of transglutaminase activity using polystyrene microtiter plates coated with N,N'-dimethylcasein. The substrate 5-(biotinamido)pentylamine is covalently incorporated into N,N'-dimethylcasein by transglutaminase in a calcium-dependent reaction. The biotinylated product is detected by streptavidin-alkaline phosphatase and quantitated by measuring the absorbance at 405 nm following the addition of p-nitrophenyl phosphate. The assay is sensitive, specific, and linear at plasma factor XIIIa concentrations between 0.08 and 1.25 micrograms/ml and at purified guinea pig liver transglutaminase concentrations between 0.05 and 0.8 microgram/ml. The intra-assay coefficient of variation is less than 8%. The solid-phase assay was used to quantitate the transglutaminase activity in Escherichia coli extracts expressing recombinant factor XIII A-chains and to analyze factor XIIIa inhibitors. This method will facilitate the analysis of structure-function relationships of the transglutaminases using recombinant DNA methods. Furthermore, screening of natural and synthetic factor XIIIa inhibitors will be expedited by this solid-phase microtiter plate assay.

ConcentrationVolumeMass	1 mg	5 mg	10 mg
1 mM	3.0444 mL	15.2221 mL	30.4442 mL
5 mM	0.6089 mL	3.0444 mL	6.0888 mL
10 mM	0.3044 mL	1.5222 mL	3.0444 mL

5-(Biotinamido)pentylamine, provides a flexible aliphatic spacer terminating in a biotinamide-derived functionality that can be used to connect targeting and E3 ligase–recruiting modules in targeted protein degradation constructs. Its amine handle supports robust conjugation strategies, while the amide linkage contributes conformational stability and predictable chemical reactivity. The linker is particularly useful for researchers optimizing linker length, polarity, and attachment chemistry in PROTAC assembly; detailed structural and synthetic considerations are provided below.

Structure: The linker contains a saturated, flexible pentyl chain bearing a terminal primary amine and a biotinamide motif. It features an amide bond that can engage in hydrogen bonding and modulate local conformation, alongside aliphatic C–C and C–N single bonds that provide rotational freedom for productive ternary complex formation.

Reactivity: The primary amine enables formation of amide or urea linkages with activated carboxylic acids (for example, via common coupling reagents) or with activated carbonyl derivatives. Biotinamide functionalities are typically preserved under standard amide-coupling conditions, provided chemoselectivity is maintained. For PROTAC construction, reactions are commonly performed under inert or controlled atmosphere in polar aprotic solvents, using base and coupling reagents compatible with amide formation, followed by purification to remove excess reagents and side products.

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* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C₁V₁ = C₂V₂