N-(Azido-PEG3)-N-Boc-PEG3-NHS ester
CAS No.: 2112731-51-6
Cat No.: BP-500449
Purity: 98%
4.5 
N-(Azido-PEG3)-N-Boc-PEG3-NHS ester is a heterobifunctional, PEG-based PROTAC linker featuring an NHS-activated ester for amide coupling and a terminal azide handle for orthogonal bioorthogonal conjugation. Structurally, it contains two short PEG3 segments that provide aqueous solubility, conformational flexibility, and a defined spacer length between the reactive ends, while the Boc-protected amine enables controlled functionalization and can be deprotected under standard conditions when required for subsequent coupling steps. In PROTAC design, the NHS ester allows efficient attachment to primary amines on a ligand, targeting moiety, or intermediate scaffold, forming a stable amide bond, whereas the azide group can be used for strain-promoted or copper-catalyzed azide–alkyne cycloaddition to install a complementary partner. This combination supports modular assembly of targeted protein degraders, improves linker tunability, and facilitates systematic structure–activity studies by enabling rapid, orthogonal conjugation workflows.
Structure of 2112731-51-6
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This N-(Azido-PEG3)-N-Boc-PEG3-NHS ester is a bifunctional PEG-based linker designed for modular PROTAC assembly, combining an NHS-activated ester for efficient conjugation and a terminal azide handle for orthogonal click chemistry. Its PEG segments provide conformational flexibility and improved solubility, supporting productive formation of ternary complexes. The azide enables site-specific attachment to complementary partners under mild conditions, while the protected amine functionality facilitates controlled downstream coupling. Detailed structural and reactivity considerations are provided below.
Structure: The linker contains PEG oligomer segments connected through ether linkages, providing hydrophilicity and chain flexibility. An NHS-activated carboxylate enables acyl transfer to nucleophiles, while an azide provides a bioorthogonal functional group for cycloaddition. A Boc-protected amine supports orthogonal reactivity and controlled deprotection prior to further coupling.
Reactivity: The NHS ester reacts with primary amines or other suitable nucleophiles to form stable amide bonds, typically using an amine-containing acceptor in mildly basic aqueous or mixed solvent systems. The azide is compatible with copper-free or copper-catalyzed azide–alkyne cycloaddition, depending on the partner and desired selectivity. Boc groups are removed under standard acidolysis conditions when subsequent amide or urea-forming steps are required; catalysts and solvents are chosen to preserve the NHS functionality until coupling is complete.
* 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
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