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2i4u

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[[Image:2i4u.jpg|left|200px]]<br /><applet load="2i4u" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2i4u, resolution 1.50&Aring;" />
 
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'''HIV-1 protease with TMC-126'''<br />
 
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==Overview==
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==HIV-1 protease with TMC-126==
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The introduction of human immunodeficiency virus type 1 (HIV-1) protease, inhibitors (PIs) markedly improved the clinical outcome and control of, HIV-1 infection. However, cross-resistance among PIs due to a wide, spectrum of mutations in viral protease is a major factor limiting their, broader clinical use. Here we report on the suppression of PI resistance, using a covalent attachment of a phosphonic acid motif to a peptidomimetic, inhibitor scaffold. The resulting phosphonate analogs maintain high, binding affinity to HIV-1 protease, potent antiretroviral activity, and, unlike the parent molecules, display no loss of potency against a panel of, clinically important PI-resistant HIV-1 strains. As shown by, crystallographic analysis, the phosphonate moiety is highly exposed to, solvent with no discernable interactions with any of the enzyme active, site or surface residues. We term this effect "solvent anchoring" and, demonstrate that it is driven by a favorable change in the inhibitor, binding entropy upon the interaction with mutant enzymes. This type of, thermodynamic behavior, which was not found with the parent scaffold fully, buried in the enzyme active site, is a result of the increased degeneracy, of inhibitor binding states, allowing effective molecular adaptation to, the expanded cavity volume of mutant proteases. This strategy, which is, applicable to various PI scaffolds, should facilitate the design of novel, PIs and potentially other antiviral therapeutics.
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<StructureSection load='2i4u' size='340' side='right'caption='[[2i4u]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2i4u]] 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=2I4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I4U FirstGlance]. <br>
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2I4U 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 <scene name='pdbligand=DJR:'>DJR</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/HIV-1_retropepsin HIV-1 retropepsin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.16 3.4.23.16] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I4U OCA].
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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]] 1.5&#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=DJR:(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL+[(1S,2R)-1-BENZYL-2-HYDROXY-3-{ISOBUTYL[(4-METHOXYPHENYL)SULFONYL]AMINO}PROPYL]CARBAMATE'>DJR</scene></td></tr>
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==Reference==
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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=2i4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i4u OCA], [https://pdbe.org/2i4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i4u RCSB], [https://www.ebi.ac.uk/pdbsum/2i4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i4u ProSAT]</span></td></tr>
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Suppression of HIV-1 protease inhibitor resistance by phosphonate-mediated solvent anchoring., Cihlar T, He GX, Liu X, Chen JM, Hatada M, Swaminathan S, McDermott MJ, Yang ZY, Mulato AS, Chen X, Leavitt SA, Stray KM, Lee WA, J Mol Biol. 2006 Oct 27;363(3):635-47. Epub 2006 Aug 2. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16979654 16979654]
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</table>
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[[Category: HIV-1 retropepsin]]
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== Function ==
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[https://www.uniprot.org/uniprot/Q7SSI0_9HIV1 Q7SSI0_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/i4/2i4u_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=2i4u ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[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: Hatada, M.]]
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[[Category: Hatada M]]
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[[Category: DJR]]
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[[Category: hydrolase]]
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[[Category: protein inhibitor complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 13:51:35 2008''
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Current revision

HIV-1 protease with TMC-126

PDB ID 2i4u

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