a Protein Data Bank extension database of pKa and pI theoretical values

pKa values of ionizable residues and isoelectric points of proteins provide valuable local and global insights about their structure and function. These properties can be estimated with reasonably good accuracy using Poisson-Boltzmann and Monte Carlo calculations at a considerable computational cost (from some minutes to several hours). pKPDB is a database of theoretical pKa values and pIs calculated over protein structures deposited in the Protein Data Bank.

10M pKa values

Calculated by using PypKa with default parameters (Ɛ = 15) on ~70% of the Protein Data Bank

120k Isoelectric Points

Determined from the theoretical titration curve accounting for the individual pka values of all titrable residues of each protein


Was pKPDB helpful in your research? Please cite:
Reis et al. Bioinformatics 2021
DOI: 10.1093/bioinformatics/btab518

Isoelectric Points

120k proteins
(csv file with ~1MB)


pKa values

10M residues
(csv file with ~61MB)


Similarity Clusters

Sequence identity > 0.9
(csv file with ~48MB)



Download vs Query

Are you interested in querying individual proteins by PDB ID instead of downloading the full database?

Use the Pypka Server

The PypKa Server is a free resource that is open to all users, including commercial users.