5P59: Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 234

Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that successfully pass clinical trials. At the heart of the screening for fragments binding to a specific target, crystallography delivers structural information essential for subsequent drug design. While it is common to search for bound ligands in electron densities calculated directly after an initial refinement cycle, we raise the important question whether this strategy is viable for fragments characterized by low affinities. Here, we describe and provide a collection of high-quality diffraction data obtained from 364 protein crystals treated with diverse fragments. Subsequent data analysis showed that approximately 25% of all hits would have been missed without further refining the resulting structures. To enable fast and reliable hit identification, we have designed an automated refinement pipeline that will inspire the development of optimized tools facilitating the successful application of fragment-based methods.
PDB ID: 5P59Download
MMDB ID: 141860
PDB Deposition Date: 2016/6/28
Updated in MMDB: 2016/08
Experimental Method:
x-ray diffraction
Resolution: 1.18  Å
Source Organism:
Similar Structures:
Biological Unit for 5P59: monomeric; determined by author and by software (PISA)
Molecular Components in 5P59
Label Count Molecule
Protein (1 molecule)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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