pkatyper - Ligand pKa


Assessment of ligand pKas can be broken into two phases. The first phase is enumeration of the protonation states of interest, and the second phase is assigning a pKa value to each of these states. An intermediate phase of assigning microscopic pKas to each of the atomic-deprotonations may also be considered.

It is common in the course of modeling small-molecules to explore the conformational ensemble of the small molecule. Often structures as high as 5-8 kcal/mol above the aqueous ground-state can be important to biological processes. It is also appropriate to enumerate a protonation-state ensemble of the small molecule.

Similar to tautomers, OpenEye has a solution for enumerating reasonable protonation states, but not for assessing the energetics of the state (e.g. assigning a pKa value). OpenEye’s solution for pKa enumeration seeks to enumerate all of the pKa states that fall roughly in the pH range of 2-14 in aqueous solvent. This range of pKa values generates an ensemble that includes the ground-state plus all charge states within 8 kcals/mol \(\Delta G\). This value was chosen to correspond to the similar range that is often used for generating conformational ensembles of small molecules.


pkatyper enumerates charge states based on primary, secondary and tertiary atom types of each atom in a molecule. The primary atom type is based on the atom’s group and its valence. The primary atom-type defines the atom’s basic propensity to support a formal charge. The secondary atom-type is defined by the atom-type of the neighbors for each atom. These secondary atom-types, such as aromaticity, alpha-beta unsaturation, or electronegative-groups, modulate each atom’s basic propensity to support formal charges. The tertiary atom-types assess the effects of nearby formal charges on a given atom’s formal charge. The combination of the primary, secondary and tertiary atom-types determine which formal charge states are allowed for each atom in a molecule. The primary and secondary atom-types are determined once, while the tertiary atom-types are determined as part of the enumeration process.

pkatyper is a rudimentary approach to pKa prediction. While pkatyper is not suited for prediction of absolute pKas, it is quite amenable to enumeration of all reasonable charge states of a very wide variety of small-molecule chemistries.

pkatyper is not a conformer generation program and will not create coordinates for molecules that are read in without coordinates. When used on molecules with three-dimensional coordinates, pkatyper attempts to place new hydrogens in a reasonable manner. However, pkatyper does not modify the heavy-atom coordinates of the molecule. In cases where the change in protonation-state dictates a change in conformation, one will need to use a conformer-generation tool (such as OMEGA) to generate reasonable conformations for the output from pkatyper. We recommend that in preparation of small-molecules for study, charge-state and tautomer enumeration be performed before conformer generation.

In the future, OpenEye will release a product which assigns a pKa value to each of the enumerated states.