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PanDDA analysis of BRD1 screened against 3D-Fragment-Consortium Fragment Library (HTML Summary)

Interactive summary page for "PanDDA analysis of BRD1 screened against 3D-Fragment-Consortium Fragment Library". Please click on "0_index.html" in the "Files" section to open the interactive summary. All datasets are also available as combined zip files from https://zenodo.org/record/48769 .

PanDDA analysis of JMJD2D screened against Zenobia Fragment Library (HTML Summary)

Interactive summary page for "PanDDA analysis of JMJD2D screened against Zenobia Fragment Library". Please click on "0_index.html" in the "Files" section to open the interactive summary. All datasets are also available as combined zip files from https://zenodo.org/record/48770 .

PanDDA analysis of SP100 screened against selection of Maybridge Fragment Library (HTML Summary)

Interactive summary page for "PanDDA analysis of SP100 screened against selection of Maybridge Fragment Library". Please click on "0_index.html" in the "Files" section to open the interactive summary. All datasets are also available as combined zip files from https://zenodo.org/record/48771 .

PanDDA analysis of BAZ2B screened against Zenobia Fragment Library (HTML Summary)

Interactive summary page for "PanDDA analysis of BAZ2B screened against Zenobia Fragment Library". Please click on "0_index.html" in the "Files" section to open the interactive summary. All datasets are also available as combined zip files from https://zenodo.org/record/48768 .

opencc-by-4.0Nov 2017View details →

PanDDA analysis of PTP1B screened against fragment libraries

Tyrosine phosphatase, PTP1B, screened against multiple fragment libraries via X-ray crystallography.

PanDDA analysis of SP100 screened against selection of Maybridge Fragment Library

Nulear auto-antigen SP-100 screened against a selection of the Maybridge Fragment Library by X-ray crystallography.

PanDDA analysis of BRD1 screened against 3D-Fragment-Consortium Fragment Library

Bromodomain BRD1 screened against the 3D Fragment Consortium Fragment Library by X-ray Crystallography.

opencc-by-4.0Jan 2017View details →

PanDDA analysis of JMJD2D screened against Zenobia Fragment Library - HTML Summary

De-methylase JMJD2D screened against the Zenobia Fragment Library by X-ray Crystallography.

opencc-by-4.0Apr 2021View details →

PanDDA analysis of fragment screen against the Nsp3 macrodomain of SARS-CoV-2 - P43 crystals at UCSF

This deposition contains the X-ray diffraction data used for the PanDDA analysis of the fragment screen against the NSP3 macrodomain of SARS-CoV-2 described in Schuller et al. 2021 (DOI: 10.1126/sciadv.abf8711). A description of the files can be found in the "README" text file.  The data in this deposition is from the fragment screen performed at UCSF using P43 crystals. The data from the fragment screen performed at UCSF using C2 crystals can be found here - https://zenodo.org/record/4716363 - in the zipped directory named "ucsf_nsp3_mac1_C2.zip".

opencc-by-4.0Jun 2022View details →

PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from fragment merging/linking and virtual screening

This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Gahbauer et al. 2022 (doi: https://doi.org/10.1101/2022.06.27.497816). mac1_pandda.zip contains the structure factor intensities, PanDDA input/ouput and refined models/maps. A description of the files can be found in the README file.  mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files.

opencc-by-4.0Jun 2018View details →

PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries

<a href="https://www.thesgc.org/scientists/groups/oxford">SGC Oxford</a> has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (<a href="http://www.uniprot.org/uniprot/P0C024">UniProtKB - P0C024</a>). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the <a href="https://www.thesgc.org/fragment-screening">SGC fragment screening website</a>. This work is part of the <a href="https://www.thesgc.org/tep">Target Enabling Package (TEP)</a> program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.   Experiment Crystals were prepared at the <a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html">XChem </a>facility of the <a href="http://www.diamond.ac.uk">Diamond Light Source</a> (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the <a href="https://xchem.github.io/oxxchem/">OxXChem</a> 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 <a href="http://www.diamond.ac.uk/Beamlines/Mx.html">MX beamlines at DLS</a>. 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.   Content This repository contains: <ul> <li>all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures</li> <li>MTZ and AIMLESS logfiles from auto-processing</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>final refine.pdb and refine.mtz filess of all ligand bound structures</li> <li>all data belonging to an individual crystal can be found in processed_datasets/<crystal_ID></li> </ul>   References 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, 2322–2330 (2016). Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).

opencc-by-4.0Oct 2018View details →

PanDDA analysis of NUDT5 screened against DSPi poised fragment library

A crystallographic fragment screen on the human ADP-sugar pyrophosphatase NUDT5 (UniProtKB - Q9UKK9) has been performed at the Structural Genomics Consortium (SGC). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID G_1002057. The final structures and the relevant PanDDA event maps can be found at the <a href="https://www.thesgc.org/fragment-screening">SGC fragment screening website</a>.   Experiment The experiment has been performed at the XChem facility at the Diamond Light Source. NUDT5 crystals were soaked with concentrated solutions (500 mM) of fragments from DSPi poised fragment library at 10% v/v for 30 minutes. All datasets were collected at I04-1 at DLS. 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.   Content This repository contains: <ul> <li>all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures</li> <li>MTZ and AIMLESS logfiles from auto-processing</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>final refine.pdb and refine.mtz filess of all ligand bound structures</li> <li>all data belonging to an individual crystal can be found in processed_datasets/<crystal_ID</li> </ul> References 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, 2322–2330 (2016). Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).

opencc-by-4.0Sep 2018View details →

PanDDA analysis of DCP2B screened against DSPL/DSi Poised, OxXChem fragment libraries and initial follow up chemistry

<a href="https://www.thesgc.org/scientists/groups/oxford">SGC Oxford</a> has performed a crystallographic fragment screen, and initial follow up chemistry on the Human m7GpppN-mRNA Hydrolase (DCP2/NUDT20, <a href="https://www.uniprot.org/uniprot/Q8IU60">UniProtKB - QIU60</a>). All structures with clearly identifiable ligands were deposited in the <a href="http://www.wwpdb.org/">Protein Data Bank</a> under Group Deposition ID G_1002061, the corresponding apo structures are deposited under Group Deposition ID G_1002062. Experiment Crystals were prepared at the <a href="http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html">XChem </a>facility of the <a href="http://www.diamond.ac.uk">Diamond Light Source</a> (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the <a href="https://xchem.github.io/oxxchem/">OxXChem</a> set with nominal fragment concentrations of 100 mM, with DMSO at 20% 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 10-200 mM, with DMSO at 20% v/v. All datasets were collected at <a href="http://www.diamond.ac.uk/Beamlines/Mx.html">MX beamlines at DLS</a>. 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. Content This repository contains: Modelled Data <ul> <li>Organised by crystal identifier, each folder contains: <ul> <li>Autoprocessing data from Diamond Light Source automated pipelines (including MTZ)</li> <li>PDB, CIF & PNG files of all the soaked compounds</li> <li>PanDDA event maps</li> <li>Final refine.pdb and refine.mtz files of all ligand bound structure <ul> <li>Superposed structures (refine.pdb)</li> <li>Separated bound & ground states (refine.split.bound.pdb & refine.split.ground.pdb)</li> </ul> </li> </ul> </li> </ul> PanDDA Analysis Data <ul> <li>This is split into two directories. This split is only due to technical limitations at the time of preparation of the data, and the timeliness of the data. <ul> <li>All results from the PanDDA analysis, including ground-state-mean maps and PanDDA event & Z-maps for all ligand bound structures. </li> </ul> </li> </ul>

opencc-by-4.0Nov 2022View details →

PanDDA analysis of PTP1B re-screened against fragment libraries at RT

PTP1B re-screened against multiple fragment libraries with RT crystallography

PanDDA analysis of JMJD2D screened against Zenobia Fragment Library

De-methylase JMJD2D screened against the Zenobia Fragment Library by X-ray Crystallography.

PanDDA analysis of BAZ2B screened against Zenobia Fragment Library

Bromodomain BAZ2B screened against the Zenobia Fragment Library by X-ray Crystallography.

opencc-by-4.0Aug 2024View details →

PanDDA analysis of ligand screen against the NSP3 macrodomain of SARS-CoV-2: ligands from FrankenROCS fragment-linking pipeline and subsequent optimization of AVI-313

This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Correy et al. 2024 (doi: https://doi.org/10.1101/2024.08.25.609621). Compounds were from fragment linking using FrankenROCS and subsequent optimization of AVI-313.  frankenROCS_mac1.tar.gz contains structure factor intensities, PanDDA input/output and refined models/maps. frankenROCS_mac1_ligand-bound-states.tar.gz contains the ligand-bound states extracted from the multi-state PDB files.