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bioRxiv · 10.1101/2025.06.08.658527

A Cryptic Interfacial Pocket Uncovered in Full CRL4CRBN-IKZF3 Ubiquitylation Complex Enhances IMiD Efficacy

Deng, Z.·Ai, H.·Shi, Q.·Liang, J.·He, Z.·Zheng, J.·Li, H.·Zhang, L.·He, W.·Tao, S.·Zheng, Q.·Pan, M.·Liu, L.
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Abstract

Immunomodulatory imide drugs (IMiDs) redirect the CUL4-RBX1-DDB1-CRBN (CRL4CRBN) ligase to ubiquitylate and degrade disease-linked proteins, but the full picture of how IMiDs glue the neosubstrate within the whole CRL4CRBN complex remains unknown. We determined cryo-electron microscopy structures of eight approved or clinical IMiDs in full CRL4CRBN ubiquitylation complexes at resolutions up to 3.4 [A], and revealed how these structurally distinct IMiDs exploit the structural plasticity of CRL4CRBN to organize conformationally conserved and compact active ubiquitylation assemblies with the neosubstrate IKZF3. Four "next-generation" IMiDs were found to additionally engage a cryptic gluing-driven interfacial (GDI) pocket at the non-degron zinc finger 3 (ZF3) of IKZF3, which contributes to their enhanced efficacy and neosubstrate specificity. The identification of cryptic gluing-driven pockets formed only in full ubiquitylation complexes provides new structure-directed design opportunities for IMiDs to improve therapeutic efficacy.

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Deng, Z., Ai, H., Shi, Q., Liang, J., He, Z., Zheng, J., Li, H., Zhang, L., He, W., Tao, S., Zheng, Q., Pan, M., Liu, L.. 2025-06-09. A Cryptic Interfacial Pocket Uncovered in Full CRL4CRBN-IKZF3 Ubiquitylation Complex Enhances IMiD Efficacy. https://doi.org/10.1101/2025.06.08.658527

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