5n3v

Thermolysin in complex with inhibitor JC292

spinqualitylabelsall models 5n3v, resolution 1.12Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5n3v is a 1 chain structure with sequence from Bacillus thermoproteolyticus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.12Å Ligands: 8L5, CA, DMS, MPD, ZN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function THER_BACTH Extracellular zinc metalloprotease. Publication Abstract from PubMed In lead optimization, open, solvent-exposed protein pockets are often disregarded as prospective binding sites. Because of bulk-solvent proximity, researchers are instead enticed to attach charged polar groups at inhibitor scaffolds to improve solubility and pharmacokinetic properties. It is rarely considered that solvent effects from water reorganization in the first hydration shell of protein-ligand complexes can have a significant impact on binding. We investigate the thermodynamic fingerprint of thermolysin inhibitors featuring terminal charged ammonium groups that are gradually pulled from a distal, solvent-exposed position into the flat, bowl-shaped S2' pocket. Even for the most remote attachment, costs for partial desolvation of the polar group next to the protein-solvent interface are difficult to compensate by interactions with the protein or surrounding water molecules. Through direct comparison with hydrophobic analogues, a significant 180-fold affinity loss was recorded, which questions popular strategies to attach polar ligand-solubilizing groups at the exposed terminus of substituents accommodated in flat open pockets. Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Distal Solubilizing Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors.,Cramer J, Krimmer SG, Heine A, Klebe G J Med Chem. 2017 Jul 13;60(13):5791-5799. doi: 10.1021/acs.jmedchem.7b00490. Epub, 2017 Jun 22. PMID:28590130 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Thermolysin 3D structures

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