View source for 9dhl


==X-ray crystal structure of AmpC beta-lactamase with inhibitor==
<StructureSection load='9dhl' size='340' side='right'caption='[[9dhl]], [[Resolution|resolution]] 1.88&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9dhl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9DHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9DHL FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.88&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1AU5:3-chloranyl-~{N}-(1-ethanoyl-2,3-dihydroindol-4-yl)-2-oxidanyl-benzenesulfonamide'>A1AU5</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=9dhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9dhl OCA], [https://pdbe.org/9dhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9dhl RCSB], [https://www.ebi.ac.uk/pdbsum/9dhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9dhl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/AMPC_ECOLI AMPC_ECOLI] This protein is a serine beta-lactamase with a substrate specificity for cephalosporins.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Virtual ligand libraries for ligand discovery have recently increased 10,000-fold. Whether this has improved hit rates and potencies has not been directly tested. Meanwhile, typically only dozens of docking hits are assayed, clouding hit-rate interpretation. Here we docked a 1.7 billion-molecule virtual library against beta-lactamase, testing 1,521 new molecules and comparing the results to a 99 million-molecule screen where 44 molecules were tested. In a larger screen, hit rates improved twofold, more scaffolds were discovered and potency improved. Fifty-fold more inhibitors were found, supporting the idea that the large libraries harbor many more ligands than are being tested. In sampling smaller sets from the 1,521, hit rates only converged when several hundred molecules were tested. Hit rates and affinities improved steadily with docking score. It may be that as the scale of docking libraries and their testing grows, both ligands and our ability to rank them will improve.

The impact of library size and scale of testing on virtual screening.,Liu F, Mailhot O, Glenn IS, Vigneron SF, Bassim V, Xu X, Fonseca-Valencia K, Smith MS, Radchenko DS, Fraser JS, Moroz YS, Irwin JJ, Shoichet BK Nat Chem Biol. 2025 Jan 3. doi: 10.1038/s41589-024-01797-w. PMID:39753705<ref>PMID:39753705</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9dhl" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Liu F]]
[[Category: Shoichet BK]]