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2q54

From Proteopedia

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(New page: 200px<br /> <applet load="2q54" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q54, resolution 1.85&Aring;" /> '''Crystal structure o...)
Current revision (13:53, 13 March 2024) (edit) (undo)
 
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[[Image:2q54.gif|left|200px]]<br />
 
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<applet load="2q54" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q54, resolution 1.85&Aring;" />
 
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'''Crystal structure of KB73 bound to HIV-1 protease'''<br />
 
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==Overview==
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==Crystal structure of KB73 bound to HIV-1 protease==
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A series of novel HIV-1 protease inhibitors based on two pseudosymmetric, dipeptide isosteres have been synthesized and evaluated. The inhibitors, were designed by incorporating N-phenyloxazolidinone-5-carboxamides into, the hydroxyethylene and (hydroxyethyl)hydrazine dipeptide isosteres as P2, and P2' ligands. Compounds with (S)-phenyloxazolidinones attached at a, position proximal to the central hydroxyl group showed low nM inhibitory, activities against wild-type HIV-1 protease. Selected compounds were, further evaluated for their inhibitory activities against a panel of, multidrug-resistant protease variants and for their antiviral potencies in, MT-4 cells. The crystal structures of lopinavir (LPV) and two new, inhibitors containing phenyloxazolidinone-based ligands in complex with, wild-type HIV-1 protease have been determined. A comparison of the, inhibitor-protease structures with the LPV-protease structure provides, valuable insight into the binding mode of the new inhibitors to the, protease enzyme. Based on the crystal structures and knowledge of, structure-activity relationships, new inhibitors can be designed with, enhanced enzyme inhibitory and antiviral potencies.
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<StructureSection load='2q54' size='340' side='right'caption='[[2q54]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2q54]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q54 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]] 1.85&#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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MU1:N~2~-ACETYL-N-[(1S,3S,4S)-4-({[(5S)-3-(3-ACETYLPHENYL)-2-OXO-1,3-OXAZOLIDIN-5-YL]CARBONYL}AMINO)-1-BENZYL-3-HYDROXY-5-PHENYLPENTYL]-L-VALINAMIDE'>MU1</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2q54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q54 OCA], [https://pdbe.org/2q54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q54 RCSB], [https://www.ebi.ac.uk/pdbsum/2q54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q54 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/O38710_9HIV1 O38710_9HIV1]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q5/2q54_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q54 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2Q54 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1] with PO4, ACT and MU1 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q54 OCA].
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*[[Immunodeficiency virus protease 3D structures|Immunodeficiency virus protease 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Design and Synthesis of HIV-1 Protease Inhibitors Incorporating Oxazolidinones as P2/P2' Ligands in Pseudosymmetric Dipeptide Isosteres., Reddy GS, Ali A, Nalam MN, Anjum SG, Cao H, Nathans RS, Schiffer CA, Rana TM, J Med Chem. 2007 Sep 6;50(18):4316-28. Epub 2007 Aug 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17696512 17696512]
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[[Category: Human immunodeficiency virus 1]]
[[Category: Human immunodeficiency virus 1]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Nalam, M.N.L.]]
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[[Category: Nalam MNL]]
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[[Category: Schiffer, C.A.]]
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[[Category: Schiffer CA]]
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[[Category: ACT]]
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[[Category: MU1]]
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[[Category: PO4]]
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[[Category: drug design]]
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[[Category: hiv-1 protease]]
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[[Category: hydrolase]]
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[[Category: protease inhibitors]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 14:57:09 2007''
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Current revision

Crystal structure of KB73 bound to HIV-1 protease

PDB ID 2q54

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