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PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries

Krojer, Tobias


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        <foaf:name>Krojer, Tobias</foaf:name>
        <foaf:givenName>Tobias</foaf:givenName>
        <foaf:familyName>Krojer</foaf:familyName>
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    <dct:title>PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries</dct:title>
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    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2018</dct:issued>
    <dcat:keyword>PanDDA</dcat:keyword>
    <dcat:keyword>Crystallographic Fragment Screening</dcat:keyword>
    <dcat:keyword>Diamond Light Source beamline I04-1</dcat:keyword>
    <dcat:keyword>XChem</dcat:keyword>
    <dcat:keyword>Structural Genomics Consortium</dcat:keyword>
    <dcat:keyword>Fragment Based Lead Discovery</dcat:keyword>
    <dcat:keyword>NUDIX domain</dcat:keyword>
    <dcat:keyword>NUDT7</dcat:keyword>
    <dcat:keyword>Target Enabling Package (TEP)</dcat:keyword>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2018-06-13</dct:issued>
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    <dct:description>&lt;p&gt;&lt;strong&gt;&lt;a href="https://www.thesgc.org/scientists/groups/oxford"&gt;SGC Oxford&lt;/a&gt; has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (&lt;a href="http://www.uniprot.org/uniprot/P0C024"&gt;UniProtKB - P0C024&lt;/a&gt;). All structures with clearly identifiable ligands were deposited in the &lt;a href="http://www.wwpdb.org/"&gt;Protein Data Bank&lt;/a&gt; under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the &lt;a href="https://www.thesgc.org/fragment-screening"&gt;SGC fragment screening website&lt;/a&gt;. This work is part of the &lt;a href="https://www.thesgc.org/tep"&gt;Target Enabling Package (TEP)&lt;/a&gt; program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;em&gt;&lt;strong&gt;Experiment&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt; &lt;p&gt;Crystals were prepared at the &lt;a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html"&gt;XChem &lt;/a&gt;facility of the &lt;a href="http://www.diamond.ac.uk"&gt;Diamond Light Source&lt;/a&gt; (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the &lt;a href="https://xchem.github.io/oxxchem/"&gt;OxXChem&lt;/a&gt; set with nominal fragment concentrations of 100 mM, with DMSO at 30% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 30 mM, with DMSO at 30% v/v. All datasets were collected at &lt;a href="http://www.diamond.ac.uk/Beamlines/Mx.html"&gt;MX beamlines at DLS&lt;/a&gt;. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.&lt;/p&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;em&gt;&lt;strong&gt;Content&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt; &lt;p&gt;This repository contains:&lt;/p&gt; &lt;ul&gt; &lt;li&gt;all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event &amp;amp; Z-maps for all ligand bound structures&lt;/li&gt; &lt;li&gt;MTZ and AIMLESS logfiles from auto-processing&lt;/li&gt; &lt;li&gt;PDB, CIF &amp;amp; PNG files of all the soaked compounds&lt;/li&gt; &lt;li&gt;final refine.pdb and refine.mtz filess of all ligand bound structures&lt;/li&gt; &lt;li&gt;all data belonging to an individual crystal can be found in &lt;em&gt;processed_datasets/&amp;lt;crystal_ID&amp;gt;&lt;/em&gt;&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;&amp;nbsp;&lt;/p&gt; &lt;p&gt;&lt;em&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/em&gt;&lt;/p&gt; &lt;p&gt;Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322&amp;ndash;2330 (2016).&lt;/p&gt; &lt;p&gt;Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).&lt;/p&gt;</dct:description>
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