Bound ligand and active site protonation states are no longer a mystery with automatic protonation mode determination using fast, quantum mechanics-based, X-ray crystallographic refinement.
XModeScore, built on top of the Phenix/DivCon plugin, uses a novel, patent pending combination of advanced refinement functional and crystallographic data in order to accurately and consistently determine experimental tautomeric states, rotomers, and ligand or residue flip states. Unlike other methods which rely on energy or affinity predictions alone, XModeScore scores the actual mode found within the X-ray crystal! Protons are no longer "invisible" or "unimportant" when XModeScore is brought to bear. The method has shown itself to be useful even at lower resolutions so even low resolution data often found in drug discovery campaigns can be used!
Human Carbonic Anhydrase II + Acetazolamide (AZM) PDB 3HS4 1.1 Å
With XModeScore, you are able to automatically generate the possible tautomers in a structure and determine the correct protonation pattern for the crystal. The following example is detailed in the XModeScore publication. In this example, XModeScore was challenged with Human Carbonic Anhydrase II + Acetazolamide (AZM) as found in the 1.1 Å PDB X-ray structure 3HS4. This structure has both X-ray data and neutron diffraction data. Upon X-ray refinement, one can clearly see the greater amount of +/- density surrounding the AZM in modes 1 and 2 which are the incorrect protonation modes when compared to the neutron diffraction results found in the PDB 4G0C.
The XModeScore results shown in the table for the corresponding protonation modes 1-3 clearly differentiates between the correct mode (i.e. mode 3) and the incorrect modes (i.e. modes 1-2). This method is able to maintain this selectivity even as the data is truncated to 2.8 Å and lower resolution.
Additional information is available on the following links. If you would like to use the software for your own drug discovery efforts, please Contact Us and request a demonstration.