CR Søndergaard

G Klebe

JE Nielsen

P Czodrowski

S Dohm

Journal of Cheminformatics

PubMed

Springer - Publisher Connector

POSTER PRESENTATION Open Access
LigpKa–a database of pKa values for small
molecule ligands designed for the use in
structure-based pKa calculations
P Czodrowski1,2*, CR Søndergaard3,4, S Dohm2, G Klebe2, JE Nielsen4
From 6th German Conference on Chemoinformatics, GCC 2010
Goslar, Germany. 7-9 November 2010
Electrostatic forces play a large role in determining the
strength of protein-ligand interactions, and the calcula-
tion of pKa value shifts upon ligand binding is therefore
an important component of any accurate protein-ligand
binding calculation. However, such pKa calculations are
rarely performed in virtual screening experiments due to
the unavailability of ligand solution pKa values and the
difficulty in generating the required charge distributions
for each ligand protonation state. We present a freely
available web-based database of small-molecule pKa
values that automates the task of retrieving protonation
states and solution pKa values for small-molecule
ligands so that these can be used with tools such as
PRODRG and PDB2PQR for generating the necessary
parameters for a structure-based pKa calculation of a
protein-ligand complex. The database contains a total of
348 pKa values and represents a significant step towards
performing accurate automated pKa value calculations
in virtual screening experiments.
Author details
1Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany. 2Philipps-
University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6,
35032 Marburg, Germany. 3Department of Chemistry, University of
Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark. 4School of
Biomolecular and Biomedical Science, Conway Institute, UCD, Dublin 4,
Ireland.
Published: 19 April 2011
doi:10.1186/1758-2946-3-S1-P21
Cite this article as: Czodrowski et al.: LigpKa–a database of pKa values
for small molecule ligands designed for the use in structure-based pKa
calculations. Journal of Cheminformatics 2011 3(Suppl 1):P21.
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* Correspondence: paul.czodrowski@merck.de
1Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
Full list of author information is available at the end of the article
Czodrowski et al. Journal of Cheminformatics 2011, 3(Suppl 1):P21
http://www.jcheminf.com/content/3/S1/P21
© 2011 Czodrowski et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative
Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and
reproduction in any medium, provided the original work is properly cited.


LigpKa – a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations

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LigpKa – a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations

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