5r8m

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Current revision (11:37, 21 February 2024) (edit) (undo)
 
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<StructureSection load='5r8m' size='340' side='right'caption='[[5r8m]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
<StructureSection load='5r8m' size='340' side='right'caption='[[5r8m]], [[Resolution|resolution]] 1.39&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5r8m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R8M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5R8M FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5r8m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5R8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5R8M FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S8G:1-[(3~{R})-3-azanylpiperidin-1-yl]-4,4,4-tris(fluoranyl)butan-1-one'>S8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.39&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IL1B, IL1F2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=S8G:1-[(3~{R})-3-azanylpiperidin-1-yl]-4,4,4-tris(fluoranyl)butan-1-one'>S8G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r8m OCA], [http://pdbe.org/5r8m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5r8m RCSB], [http://www.ebi.ac.uk/pdbsum/5r8m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5r8m ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5r8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5r8m OCA], [https://pdbe.org/5r8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5r8m RCSB], [https://www.ebi.ac.uk/pdbsum/5r8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5r8m ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/IL1B_HUMAN IL1B_HUMAN]] Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.<ref>PMID:3920526</ref>
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[https://www.uniprot.org/uniprot/IL1B_HUMAN IL1B_HUMAN] Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.<ref>PMID:3920526</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Nowadays, it is possible to combine X-ray crystallography and fragment screening in a medium throughput fashion to chemically probe the surfaces used by proteins to interact and use the outcome of the screens to systematically design protein-protein inhibitors. To prove it, we first performed a bioinformatics analysis of the Protein Data Bank protein complexes, which revealed over 400 cases where the crystal lattice of the target in the free form is such that large portions of the interacting surfaces are free from lattice contacts and therefore accessible to fragments during soaks. Among the tractable complexes identified, we then performed single fragment crystal screens on two particular interesting cases: the Il1beta-ILR and p38alpha-TAB1 complexes. The result of the screens showed that fragments tend to bind in clusters, highlighting the small-molecule hotspots on the surface of the target protein. In most of the cases, the hotspots overlapped with the binding sites of the interacting proteins.
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Mining the PDB for Tractable Cases Where X-ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated by IL1beta-IL1R and p38alpha-TAB1 Complexes.,Nichols C, Ng J, Keshu A, Kelly G, Conte MR, Marber MS, Fraternali F, De Nicola GF J Med Chem. 2020 Jul 1. doi: 10.1021/acs.jmedchem.0c00403. PMID:32543856<ref>PMID:32543856</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5r8m" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Nichols, C E]]
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[[Category: De Nicola GF]]
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[[Category: Nicola, G F.De]]
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[[Category: Nichols CE]]
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[[Category: Il-1 beta]]
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[[Category: Pandda]]
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[[Category: Sgc - diamond i04-1 fragment screening]]
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[[Category: Signaling protein]]
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[[Category: Xchemexplorer]]
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Current revision

PanDDA analysis group deposition INTERLEUKIN-1 BETA -- Fragment Z1818332938 in complex with INTERLEUKIN-1 BETA

PDB ID 5r8m

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OCA

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