8aap: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8aap]] is a 2 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=8AAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AAP FirstGlance]. <br>
<table><tr><td colspan='2'>[[8aap]] is a 2 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=8AAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AAP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLV:(2S)-2-[[(2S)-2-(6-bromanyl-3-oxidanylidene-1H-isoindol-2-yl)-3-[4-(5-ethanoyl-2-fluoranyl-phenyl)phenyl]propanoyl]amino]propanoic+acid'>LLV</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.174&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLV:(2S)-2-[[(2S)-2-(6-bromanyl-3-oxidanylidene-1H-isoindol-2-yl)-3-[4-(5-ethanoyl-2-fluoranyl-phenyl)phenyl]propanoyl]amino]propanoic+acid'>LLV</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=8aap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8aap OCA], [https://pdbe.org/8aap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8aap RCSB], [https://www.ebi.ac.uk/pdbsum/8aap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8aap ProSAT]</span></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=8aap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8aap OCA], [https://pdbe.org/8aap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8aap RCSB], [https://www.ebi.ac.uk/pdbsum/8aap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8aap ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/SDCB1_HUMAN SDCB1_HUMAN] Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.<ref>PMID:10230395</ref> <ref>PMID:11179419</ref> <ref>PMID:11498591</ref>  
[https://www.uniprot.org/uniprot/SDCB1_HUMAN SDCB1_HUMAN] Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.<ref>PMID:10230395</ref> <ref>PMID:11179419</ref> <ref>PMID:11498591</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The rapid identification of early hits by fragment-based approaches and subsequent hit-to-lead optimization represents a challenge for drug discovery. To address this challenge, we created a strategy called "DOTS" that combines molecular dynamic simulations, computer-based library design (chemoDOTS) with encoded medicinal chemistry reactions, constrained docking, and automated compound evaluation. To validate its utility, we applied our DOTS strategy to the challenging target syntenin, a PDZ domain containing protein and oncology target. Herein, we describe the creation of a "best-in-class" sub-micromolar small molecule inhibitor for the second PDZ domain of syntenin validated in cancer cell assays. Key to the success of our DOTS approach was the integration of protein conformational sampling during hit identification stage and the synthetic feasibility ranking of the designed compounds throughout the optimization process. This approach can be broadly applied to other protein targets with known 3D structures to rapidly identify and optimize compounds as chemical probes and therapeutic candidates.


Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach.,Hoffer L, Garcia M, Leblanc R, Feracci M, Betzi S, Ben Yaala K, Daulat AM, Zimmermann P, Roche P, Barral K, Morelli X J Med Chem. 2023 Apr 13;66(7):4633-4658. doi: 10.1021/acs.jmedchem.2c01569. Epub , 2023 Mar 20. PMID:36939673<ref>PMID:36939673</ref>
==See Also==
 
*[[3D structures of syntenin|3D structures of syntenin]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8aap" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 11:10, 7 February 2024

Crystal structure of the PDZ tandem of syntenin in complex with compound SYNTiCrystal structure of the PDZ tandem of syntenin in complex with compound SYNTi

Structural highlights

8aap is a 2 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.174Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDCB1_HUMAN Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.[1] [2] [3]

See Also

References

  1. ↑ Fernandez-Larrea J, Merlos-Suarez A, Urena JM, Baselga J, Arribas J. A role for a PDZ protein in the early secretory pathway for the targeting of proTGF-alpha to the cell surface. Mol Cell. 1999 Apr;3(4):423-33. PMID:10230395
  2. ↑ Zimmermann P, Tomatis D, Rosas M, Grootjans J, Leenaerts I, Degeest G, Reekmans G, Coomans C, David G. Characterization of syntenin, a syndecan-binding PDZ protein, as a component of cell adhesion sites and microfilaments. Mol Biol Cell. 2001 Feb;12(2):339-50. PMID:11179419
  3. ↑ Geijsen N, Uings IJ, Pals C, Armstrong J, McKinnon M, Raaijmakers JA, Lammers JW, Koenderman L, Coffer PJ. Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein. Science. 2001 Aug 10;293(5532):1136-8. PMID:11498591 doi:http://dx.doi.org/10.1126/science.1059157

8aap, resolution 2.17Å

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