bioRxiv2026
The rapid expansion of high-resolution cryo-EM structures of amyloid fibrils has transformed our understanding of fibril polymorphism, yet it has not been matched by comparable progress in the rational development of protein-selective or polymorph-specific amyloid ligands. One possible explanation is that ligand selectivity is governed not only by global fibril folds, but also by local surface pockets accessible to small molecules. Here, we present a systematic analysis of 400 cryo-EM structures of amyloid-{beta}, tau, and -synuclein fibrils. Using a unified pocket similarity index and minimum spanning tree representations, we construct global and protein-specific graph representations of the amyloid binding pocket space, and examine how surface cavities are distributed across proteins, polymorphs, and structural contexts. We find that many detectable pockets are shared across multiple fibrillar folds and, in several cases, across distinct amyloid-forming proteins, suggesting that pocket-level convergence may contribute to the limited selectivity of amyloid-directed ligands. Conversely, only a restricted subset of pockets occupies isolated regions of pocket similarity space, defining rare structural opportunities for protein-selective or polymorph-restricted targeting. Analysis of structures of extracted fibrils further shows that disease-derived fibril pockets do not form a completely isolated pocketome subset, but can resemble pockets observed in selected in vitro polymorphs. Together, these results reframe amyloid ligand development as a problem of pocket-level discriminability within a constrained fibril landscape, and provide a structural framework for identifying promising binding sites while avoiding intrinsically non-discriminatory pockets. Significance StatementDespite major advances in cryo-EM structure determination of amyloid fibrils, the development of selective ligands for amyloid assemblies remains challenging. By systematically comparing surface binding pockets across 400 amyloid-{beta}, tau, and -synuclein fibrillar structures, we show that many ligand-accessible cavities exhibit similar geometric and physicochemical properties across fibrillar polymorphs made of distinct proteins. This pocket-level convergence provides a structural basis for understanding why many amyloid ligands exhibit broad binding profiles, while also identifying rare pockets that are sufficiently isolated to support more selective targeting strategies. Our work establishes a pocket-centric framework for interpreting amyloid ligand selectivity and for prioritizing fibril binding sites in imaging and therapeutic ligand development.