4dvv: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4dvv]] 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=4DVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVV FirstGlance]. <br>
<table><tr><td colspan='2'>[[4dvv]] 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=4DVV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DVV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0M1:N-{[(4S,5S)-5-(AMINOMETHYL)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL}-N-(4-CHLORO-3-FLUOROPHENYL)ETHANEDIAMIDE'>0M1</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.94&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0M1:N-{[(4S,5S)-5-(AMINOMETHYL)-2,2-DIMETHYL-1,3-DIOXOLAN-4-YL]METHYL}-N-(4-CHLORO-3-FLUOROPHENYL)ETHANEDIAMIDE'>0M1</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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4dvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvv OCA], [https://pdbe.org/4dvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvv RCSB], [https://www.ebi.ac.uk/pdbsum/4dvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvv ProSAT]</span></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=4dvv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dvv OCA], [https://pdbe.org/4dvv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dvv RCSB], [https://www.ebi.ac.uk/pdbsum/4dvv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dvv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]]
[https://www.uniprot.org/uniprot/A0A0M3KKW9_9HIV1 A0A0M3KKW9_9HIV1]  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4dvv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Gp120 3D structures|Gp120 3D structures]]
*[[Gp120 3D structures|Gp120 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Revision as of 17:46, 14 March 2024

Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-I-261Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AS-I-261

Structural highlights

4dvv is a 2 chain structure with sequence from Human immunodeficiency virus 1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.94Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0M3KKW9_9HIV1

See Also

4dvv, resolution 1.94Å

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