5n2x: Difference between revisions
New page: '''Unreleased structure''' The entry 5n2x is ON HOLD until Paper Publication Authors: Cramer, J., Krimmer, S.G., Heine, A., Klebe, G. Description: Thermolysin in complex with inhibitor... |
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==Thermolysin in complex with inhibitor JC272== | |||
<StructureSection load='5n2x' size='340' side='right'caption='[[5n2x]], [[Resolution|resolution]] 1.21Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5n2x]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_thermoproteolyticus Bacillus thermoproteolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5N2X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5N2X FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.209Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8KN:(2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic+acid'>8KN</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5n2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5n2x OCA], [https://pdbe.org/5n2x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5n2x RCSB], [https://www.ebi.ac.uk/pdbsum/5n2x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5n2x ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/THER_BACTH THER_BACTH] Extracellular zinc metalloprotease. | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:28590130</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5n2x" style="background-color:#fffaf0;"></div> | ||
[[Category: Heine | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Thermolysin 3D structures|Thermolysin 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus thermoproteolyticus]] | |||
[[Category: Large Structures]] | |||
[[Category: Cramer J]] | |||
[[Category: Heine A]] | |||
[[Category: Klebe G]] | |||
[[Category: Krimmer SG]] | |||
Latest revision as of 13:33, 17 January 2024
Thermolysin in complex with inhibitor JC272Thermolysin in complex with inhibitor JC272
Structural highlights
FunctionTHER_BACTH Extracellular zinc metalloprotease. Publication Abstract from PubMedIn 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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