View source for 9pal


==Crystal structure of HCoV-HKU1 3CLpro with ALG-097655 (Inhibitor 2)==
<StructureSection load='9pal' size='340' side='right'caption='[[9pal]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9pal]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_coronavirus_HKU1 Human coronavirus HKU1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9PAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9PAL 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]] 2.54&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1CHJ:(1~{R},2~{S},3~{S},6~{R},7~{S})-~{N}-[(2~{S})-1-azanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-4-[(2~{S})-4,4,4-tris(fluoranyl)-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-4-azatricyclo[5.2.1.0^{2,6}]dec-8-ene-3-carboxamide'>A1CHJ</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=9pal FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9pal OCA], [https://pdbe.org/9pal PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9pal RCSB], [https://www.ebi.ac.uk/pdbsum/9pal PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9pal ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/R1A_CVHN1 R1A_CVHN1] The papain-like proteinase 1 (PL1-PRO) and papain-like proteinase 2 (PL2-PRO) are responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PLP2 possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF-3 (By similarity).  Responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772]  Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.  Catalytic subunit of viral RNA capping enzyme which catalyzes the RNA guanylyltransferase reaction for genomic and sub-genomic RNAs. The kinase-like NiRAN domain of NSP12 transfers RNA to the amino terminus of NSP9, forming a covalent RNA-protein intermediate. Subsequently, the NiRAN domain transfers RNA to GDP, forming the core cap structure GpppA-RNA. The NSP14 and NSP16 methyltransferases then add methyl groups to form functional cap structures.[UniProtKB:P0DTC1]  Binds to the 40S ribosomal subunit and inhibits host translation. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Epidemic and pandemic outbreaks of respiratory illness caused by three different coronaviruses over the past two decades have underscored the importance of pharmaceutical agents that could offer broad-spectrum activity across this family of pathogens. Two coronavirus inhibitors characterized by broad in vitro potency were synthesized and studied with X-ray crystallography. Their high-resolution structures in complex with six alpha-, beta-, and gamma-coronaviruses delineate the requirements for pan-coronavirus inhibition by drug-like molecules targeting the S1-S4 subsites of the viral 3CL-protease, which performs a critical function during coronavirus polyprotein processing. Anchoring by polar contacts in S1, utilization of hydrophobic packing in S2, compact substitutions in S3, and mid-sized hydrophobic modifications in S4 are all factors contributing to inhibitor activity. Interactions in S2 are modulated by the amino acid identity of three key residues, and in S4, where sequence conservation is the lowest, pan-coronavirus coverage is facilitated by solvent exposure of the diverging side chains.

Structural basis for pan-coronavirus inhibition of 3CL protease.,Reddem ER, Forouhar F, Liu C, Stevens SK, Jekle A, Chang CW, Oswal N, McGowan DC, Vandyck K, Smith DB, Raboisson P, Beigelman LN, Katsamba PS, Bahna F, Mannepalli S, Blatt L, Perlin D, Symons JA, Shapiro L, Stoycheva AD Structure. 2026 Apr 2;34(4):562-571.e8. doi: 10.1016/j.str.2026.01.003. Epub 2026 , Feb 5. PMID:41650964<ref>PMID:41650964</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9pal" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Human coronavirus HKU1]]
[[Category: Large Structures]]
[[Category: Forouhar F]]
[[Category: Reddem ER]]
[[Category: Shapiro L]]
[[Category: Stoycheva A]]