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4dvs

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==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==
==Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557==
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<StructureSection load='4dvs' size='340' side='right' caption='[[4dvs]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='4dvs' size='340' side='right'caption='[[4dvs]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4dvs]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DVS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4dvs]] 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=4DVS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVS FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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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]] 2.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dvr|4dvr]], [[4dvt|4dvt]], [[4dvu|4dvu]], [[4dvv|4dvv]], [[4dvw|4dvw]], [[4dvx|4dvx]]</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=0LY:N-(4-BROMOPHENYL)-N-(2,2,6,6-TETRAMETHYLPIPERIDIN-4-YL)ETHANEDIAMIDE'>0LY</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [http://pdbe.org/4dvs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [http://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs ProSAT]</span></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=4dvs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvs OCA], [https://pdbe.org/4dvs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvs RCSB], [https://www.ebi.ac.uk/pdbsum/4dvs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvs ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]
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Efforts to develop therapeutic agents that inhibit HIV-1 entry have led to the identification of several small molecule leads. One of the most promising is the NBD series, which binds within a conserved gp120 cavity and possesses para-halogen substituted aromatic rings, a central oxalamide linker, and a tetramethylpiperidine moiety. In this study, we characterized structurally the interactions of four NBD analogues containing meta-fluoro substitution on the aromatic ring and various heterocyclic ring replacements of the tetramethylpiperidine group. The addition of a meta-fluorine to the aromatic ring improved surface complementarity and did not alter the position of the analogue relative to gp120. By contrast, heterocyclic ring replacements of the tetramethylpiperidine moiety exhibited diverse positioning and interactions with the vestibule of the gp120 cavity. Overall, the biological profile of NBD-congeners was modulated by ligand interactions with the gp120-cavity vestibule. Herein, six co-crystal structures of NBD-analogues with gp120 provide a structural framework for continued small molecule-entry inhibitor optimization.
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Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site.,Kwon YD, Lalonde JM, Yang Y, Elban MA, Sugawara A, Courter JR, Jones DM, Smith AB 3rd, Debnath AK, Kwong PD PLoS One. 2014 Jan 28;9(1):e85940. doi: 10.1371/journal.pone.0085940. eCollection, 2014. PMID:24489681<ref>PMID:24489681</ref>
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==See Also==
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*[[Gp120 3D structures|Gp120 3D structures]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4dvs" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Kwon, Y D]]
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[[Category: Human immunodeficiency virus 1]]
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[[Category: Kwong, P D]]
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[[Category: Large Structures]]
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[[Category: Cd4 binding site]]
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[[Category: Kwon YD]]
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[[Category: Hiv-1 gp120]]
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[[Category: Kwong PD]]
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[[Category: Nbd-557]]
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[[Category: Small molecule inhibitor]]
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[[Category: Viral protein-transcription inhibitor complex]]
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Current revision

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with NBD-557

PDB ID 4dvs

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