CovPDB is a freely accessible web database solely dedicated to high-resolution 3D structures of biologically relevant covalent protein–ligand complexes, mined from the Protein Data Bank ( https://www.rcsb.org/ ).
We have so created CovPDB to assist structure-based approaches in chemical biology and drug design by identifying covalent binding sites suitable for the docking of drug-like ligands, and, likewise, typical ligands that covalently modifying targetable binding sites. Furthermore, the corresponding covalent bonding mechanisms of such complexes were manually expertly annotated. Totally, CovPDB describes:
- 2294 covalent complexes
- 1501 pre-reactive ligands
- 733 target proteins
- 93 reactive warheads
- 21 covalent mechanisms
- 14 targetable residues
CovPDB freely provides its content as separate files for download, namely, all ligand structures (SDF format), protein sequences (FASTA format), protein-ligand complexes (PDB format), and reactive warheads (TXT format).
Mingjie Gao, Aurélien F A Moumbock, Ammar Qaseem, Qianqing Xu, Stefan Günther
CovPDB: a high-resolution coverage of the covalent protein–ligand interactome.
Nucleic Acids Res. 2022 Jan 7;50(D1):D445-D450. doi: 10.1093/nar/gkab868. PMID: 34581813; PMCID: PMC8728183.