This data deposition contains comprehensive experimental and structural data for the NCS1 project: An automated and resource-efficient synchrotron workflow for fragment-to-scaffold progression enables rapid discovery of protein–protein interaction modulators The dataset is organized into several categories: Creoptix kinetic data for ligand binding studies, including the measurement and analysis of crude reaction mixtures for the amidation and sulfonamide series and catalogue compounds. LCMS (Liquid Chromatography-Mass Spectrometry) data for compound characterization, divided into batches and series. OT-script data for automated experimental protocols, with batch-wise organization. PDB deposition files for NCS1 ligand-bound structures, including model coordinates (.cif), structure factors (.mtz, .cif), and event maps for multiple ligands. Documentation files (README) for each data type, providing details on experimental procedures and file contents.