** *Dear all,* * We are excited to announce the introduction of Covalently Linked Components (CLCs), a new class of reference small molecules that facilitates identification of covalently linked multi-component ligands across the whole PDB archive. This enhancement vastly improves the accessibility and usability of small molecule data for users. Alongside CLCs, we have further enriched the existing Peptide-like molecules Reference Dictionary (PRD) files by providing additional metadata, such as chemical properties and mapping between these molecules and other chemical data resources. As part of the update, we are also making changes to the PDBeChem FTP directory structure, aimed at enhancing user experience and making small molecule data in the Protein Data Bank in Europe (PDBe) more accessible. In this update, we have introduced separate folders for three types of reference files: Chemical Components (CCD), Covalently Linked Components (CLC), and Peptide-like molecules Reference Dictionary (PRD), making it easier for users to access specific data. The PDBeChem pipeline that powers this process and updates this data weekly, uses PDBe CCDUtils as its primary package. PDBe CCDUtils is an RDKit-based toolkit for handling and analysing small molecules in the PDB. For more information about CLC and these changes, visit:https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components <https://www.ebi.ac.uk/pdbe/news/introducing-covalently-linked-components> *Urgent Notice: *Effective from January 1st, 2024, we will be retiring the top-level sub-directories and files related to CCD (Chemical Components) as part of our ongoing updates. This decision has been made to streamline our data organisation and improve the user experience. Detailed information regarding this change is provided in the README.txt, accessible at:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/README.txt <https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/README.txt>. We value your cooperation and understanding as we strive to improve our data infrastructure and user accessibility. Thankyou for your continued support. Kind Regards, David * -- David Armstrong Outreach and Training Lead PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK