3vqb: Difference between revisions
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==HIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid== | ==HIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid== | ||
<StructureSection load='3vqb' size='340' side='right' caption='[[3vqb]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='3vqb' size='340' side='right'caption='[[3vqb]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3vqb]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3vqb]] 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=3VQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VQB FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FBG:6-FLUORO-4H-1,3-BENZODIOXINE-8-CARBOXYLIC+ACID'>FBG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=FBG:6-FLUORO-4H-1,3-BENZODIOXINE-8-CARBOXYLIC+ACID'>FBG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3vqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vqb OCA], [https://pdbe.org/3vqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vqb RCSB], [https://www.ebi.ac.uk/pdbsum/3vqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vqb ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q72498_9HIV1 Q72498_9HIV1] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
| Line 22: | Line 23: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Human immunodeficiency virus 1]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Chalmers DK]] | ||
[[Category: | [[Category: Parker MW]] | ||
[[Category: | [[Category: Scanlon MJ]] | ||
[[Category: | [[Category: Wielens J]] | ||
Latest revision as of 15:32, 8 November 2023
HIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acidHIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid
Structural highlights
FunctionPublication Abstract from PubMedFragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the HIV-1 integrase core domain (IN) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), and the other used surface plasmon resonance (SPR) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the STD-NMR/X-ray approach, 15 IN/fragment complexes were identified, whereas the SPR/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on IN that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits. Parallel Screening of Low Molecular Weight Fragment Libraries: Do Differences in Methodology Affect Hit Identification?,Wielens J, Headey SJ, Rhodes DI, Mulder RJ, Dolezal O, Deadman JJ, Newman J, Chalmers DK, Parker MW, Peat TS, Scanlon MJ J Biomol Screen. 2012 Nov 13. PMID:23139382[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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