2-(2,6-Dioxopiperidin-3-yl)-4-((9-hydroxynonyl)oxy)isoindoline-1,3-dione
CAS No.: 2619511-72-5
Cat No.: BP-502132
Purity: ≥95%
4.5 
2-(2,6-Dioxopiperidin-3-yl)-4-((9-hydroxynonyl)oxy)isoindoline-1,3-dione is a phthalimide-based PROTAC linker featuring a glutarimide-like dioxopiperidinyl amide handle and an ether-linked, nine-carbon hydroxylated alkyl spacer. The isoindoline-1,3-dione core provides a rigid, well-precedented scaffold commonly used to connect to ubiquitin ligase–recruiting modules, while the dioxopiperidinyl substituent supports controlled attachment geometry for productive ternary-complex formation. The extended hydroxynonyl segment increases conformational flexibility and distance between the ligase-binding region and the partner-binding warhead, enabling tuning of spatial alignment that is critical for efficient ubiquitination and proteasomal degradation. In targeted protein degradation research, this linker is valuable for systematic structure–activity studies, facilitating modular synthesis of PROTACs with optimized linker length and linkage orientation to improve degradation potency and selectivity across different target classes.
Structure of 2619511-72-5
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This PROTAC linker is designed to connect a protein-binding ligand to an E3-recruiting module through a stable, chemically addressable scaffold. Its combination of a cyclic imide core with a flexible ether-bearing side chain supports reliable conjugation strategies and can help maintain productive linker geometry in targeted protein degradation workflows. The sections below describe its structure and practical reactivity considerations in detail.
Structure: The linker contains an isoindoline-1,3-dione (phthalimide-like) motif and a cyclic dioxopiperidinyl substituent, providing rigid, conjugation-capable carbonyl-rich functionality. An ether linkage to a hydroxylated aliphatic chain introduces conformational flexibility. Multiple amide-imide carbonyls enable strong hydrogen-bonding and polarity.
Reactivity: For PROTAC assembly, the linker is typically used in covalent coupling sequences that exploit its functional groups for nucleophilic substitution or amide-forming steps, depending on the complementary partner. Conjugations are commonly performed under inert or controlled atmosphere, using polar aprotic solvents to promote solubility and reaction efficiency. Base-mediated activation and standard peptide-coupling reagents are often employed to form stable linkages while minimizing side reactions.
* 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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