9k2d

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'''Unreleased structure'''
 
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The entry 9k2d is ON HOLD
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==Structure of ClpP from Staphylococcus aureus in complex with ZY39==
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<StructureSection load='9k2d' size='340' side='right'caption='[[9k2d]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[9k2d]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_Mu3 Staphylococcus aureus subsp. aureus Mu3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9K2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9K2D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.98&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1EEK:(6~{S},9~{a}~{S})-6-[(2~{S})-butan-2-yl]-8-[(4-methoxynaphthalen-1-yl)methyl]-4,7-bis(oxidanylidene)-~{N}-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9~{a}-tetrahydro-2~{H}-pyrazino[1,2-a]pyrimidine-1-carboxamide'>A1EEK</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9k2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9k2d OCA], [https://pdbe.org/9k2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9k2d RCSB], [https://www.ebi.ac.uk/pdbsum/9k2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9k2d ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/CLPP_STAA1 CLPP_STAA1] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Peritonitis caused by Staphylococcus aureus poses a severe threat to patients with end-stage renal failure. Treating multidrug-resistant S. aureus infections requires the use of antibiotics with diverse mechanisms of action. Caseinolytic protease P (ClpP) is a promising antibacterial target; however, selective activation of S. aureus ClpP (SaClpP) over human ClpP (HsClpP) remains challenging. We previously identified (R)-ZG197 as a selective SaClpP agonist, but its potency was suboptimal. Herein, we develop (R)-ZG197 analogs through a structure-guided approach and examine their structure-activity relationships. Notably, ZY39 demonstrates improved activation of SaClpP and superior binding affinity. Interestingly, while ZY39 facilitates the enzymatic hydrolysis of SaClpP and HsClpP in vitro, it does not target HsClpP in cellular environments. Furthermore, ZY39 effectively inhibits the growth of multidrug-resistant S. aureus strains and shows excellent therapeutic efficacy in a murine model of peritonitis. These findings highlight ZY39 as a promising SaClpP agonist for combating staphylococcal infections.
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Authors: Wei, B.Y., Wang, P.Y., Wu, W., Zhang, T., Yang, C.-G.
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Structure-Guided Development of ClpP Agonists with Potent Therapeutic Activities against Staphylococcus aureus Infection.,Zhang T, Wu W, Zhao Y, Ding Z, Wei B, Yang T, Li J, Wang P, Lan L, Gan J, Yang CG J Med Chem. 2025 Jan 23;68(2):1810-1823. doi: 10.1021/acs.jmedchem.4c02562. Epub , 2025 Jan 6. PMID:39760203<ref>PMID:39760203</ref>
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Description: Structure of ClpP from Staphylococcus aureus in complex with ZY39
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Wang, P.Y]]
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<div class="pdbe-citations 9k2d" style="background-color:#fffaf0;"></div>
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[[Category: Zhang, T]]
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== References ==
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[[Category: Wei, B.Y]]
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<references/>
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[[Category: Wu, W]]
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__TOC__
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[[Category: Yang, C.-G]]
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Staphylococcus aureus subsp. aureus Mu3]]
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[[Category: Wang PY]]
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[[Category: Wei BY]]
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[[Category: Wu W]]
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[[Category: Yang C-G]]
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[[Category: Zhang T]]

Current revision

Structure of ClpP from Staphylococcus aureus in complex with ZY39

PDB ID 9k2d

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