About CovPDB 2.0
CovPDB is a freely accessible database of experimentally determined and computationally predicted covalent protein–ligand interactions designed to support covalent drug discovery. The database is primarily curated from high-resolution structures deposited in the Protein Data Bank (PDB).
What is new in CovPDB 2.0?
CovPDB 2.0 substantially expands the database, increasing the number of curated covalent protein–ligand complexes to nearly three times that of the previous release. This update further strengthens applications in covalent drug discovery and rational inhibitor design while extending the resource toward the systematic identification of novel covalent druggable targets.
Highlights of CovPDB 2.0
- Nearly threefold expansion of curated covalent protein–ligand complexes.
- Integration of chemoproteomics-derived ligandable human cysteine residues from CysDB.
- AlphaFold 3 models for ligandable cysteine residues.
- Predicted covalent binding sites identified through large-scale structural pocket analysis.
- Improved interactive 3D visualization for proteins and ligands.
- Expanded download section including ligand structures, protein sequences, complexes, AF3 models and reactive warheads.
Available Downloads
CovPDB provides all data free of charge, including ligand structures (SDF), protein sequences (FASTA), protein–ligand complexes (PDB), AF3 models, and reactive warhead definitions (TXT).
CovPDB 2.0 at a Glance
| Covalent Complexes | 6186 |
| Covalent PDB | 5830 |
| Pre-reactive Ligands | 3616 |
| Target Proteins | 1327 |
| Reactive Warheads | 119 |
| Covalent Mechanisms | 27 |
| Targetable Residues | 15 |
| Covalently Bound Complexes (Modeled by AF3) | 6783 |
| Non-Covalently Bound Complexes Near Cysteines | 7109 |