5epy: Difference between revisions
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==Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-mcP1P3 (MK-5172 P1-P3 macrocyclic analogue)== | ==Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-mcP1P3 (MK-5172 P1-P3 macrocyclic analogue)== | ||
<StructureSection load='5epy' size='340' side='right' caption='[[5epy]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='5epy' size='340' side='right'caption='[[5epy]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5epy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPY OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5epy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepacivirus_C Hepacivirus C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EPY FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5R2:2-METHYL-2-PROPANYL+{(2R,6S,12Z,13AS,14AR,16AS)-14A-[(CYCLOPROPYLSULFONYL)CARBAMOYL]-2-[(3-ETHYL-7-METHOXY-2-QUINOXALINYL)OXY]-5,16-DIOXO-1,2,3,5,6,7,8,9,10,11,13A,14,14A,15,16,16A-HEXADECAHYDROCYCLOP+ROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECIN-6-YL}CARBAMATE'>5R2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5R2:2-METHYL-2-PROPANYL+{(2R,6S,12Z,13AS,14AR,16AS)-14A-[(CYCLOPROPYLSULFONYL)CARBAMOYL]-2-[(3-ETHYL-7-METHOXY-2-QUINOXALINYL)OXY]-5,16-DIOXO-1,2,3,5,6,7,8,9,10,11,13A,14,14A,15,16,16A-HEXADECAHYDROCYCLOP+ROPA[E]PYRROLO[1,2-A][1,4]DIAZACYCLOPENTADECIN-6-YL}CARBAMATE'>5R2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5epy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5epy OCA], [https://pdbe.org/5epy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5epy RCSB], [https://www.ebi.ac.uk/pdbsum/5epy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5epy ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/C1KIK8_9HEPC C1KIK8_9HEPC] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</div> | </div> | ||
<div class="pdbe-citations 5epy" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5epy" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Virus protease 3D structures|Virus protease 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Hepacivirus C]] | ||
[[Category: Large Structures]] | |||
[[Category: | [[Category: Ali A]] | ||
[[Category: | [[Category: Aydin C]] | ||
[[Category: | [[Category: Prachanronarong KL]] | ||
[[Category: | [[Category: Schiffer CA]] | ||
[[Category: | [[Category: Soumana DI]] | ||
[[Category: | [[Category: Yilmaz NK]] | ||
[[Category: | |||
Latest revision as of 11:15, 12 July 2023
Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-mcP1P3 (MK-5172 P1-P3 macrocyclic analogue)Crystal structure of HCV NS3/4A protease A156T variant in complex with 5172-mcP1P3 (MK-5172 P1-P3 macrocyclic analogue)
Structural highlights
FunctionPublication Abstract from PubMedRecent advances in direct-acting antivirals against Hepatitis C Virus (HCV) have led to the development of potent inhibitors, including MK-5172, that target the viral NS3/4A protease with relatively low susceptibility to resistance. MK-5172 has a P2-P4 macrocycle and a unique binding mode among current protease inhibitors where the P2 quinoxaline packs against the catalytic residues H57 and D81. However, the effect of macrocyclization on this binding mode is not clear, as is the relation between macrocyclization, thermodynamic stabilization, and susceptibility to the resistance mutation A156T. We have determined high-resolution crystal structures of linear and P1-P3 macrocyclic analogs of MK-5172 bound to WT and A156T protease and compared these structures, their molecular dynamics and experimental binding thermodynamics to the parent compound. We find that the "unique" binding mode of MK-5172 is conserved even when the P2-P4 macrocycle is removed or replaced with a P1-P3 macrocycle. While beneficial to decreasing the entropic penalty associated with binding, the constraint exerted by the P2-P4 macrocycle prevents efficient rearrangement to accommodate the A156T mutation, a deficit alleviated in the linear and P1-P3 analogs. Design of macrocyclic inhibitors against NS3/4A needs to achieve the best balance between exerting optimal conformational constraint for enhancing potency, fitting within the substrate envelope and allowing adaptability to be robust against resistance mutations. Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172.,Soumana DI, Kurt Yilmaz N, Prachanronarong KL, Aydin C, Ali A, Schiffer CA ACS Chem Biol. 2015 Dec 18. PMID:26682473[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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