The WD40-repeat proteins are a large family of scaffold molecules that assemble complexes in various cellular processes. Obtaining their structures is the key to understanding their interaction details. We present WDSPdb 2.0, a significantly updated resource providing accurately predicted secondary and tertiary structures and featured sites annotations. Based on an optimized pipeline, WDSPdb 2.0 contains about 600 thousand entries, an increase of 10-fold, and integrates more than 37,000 variants from sources of ClinVar, Cosmic, 1000 Genomes, ExAC, IntOGen, cBioPotral, and IntAct. In addition, the web site is largely improved for visualization, exploring, and data downloading.