2qmd: Difference between revisions

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-[[Image:2qmd.jpg|left|200px]]
- {{Structure
+==Structure of BACE Bound to SCH722924==
-|PDB= 2qmd |SIZE=350|CAPTION= <scene name='initialview01'>2qmd</scene>, resolution 1.650&Aring;
+<StructureSection load='2qmd' size='340' side='right'caption='[[2qmd]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Cs7+Binding+Site+For+Residue+A+1'>AC1</scene>, <scene name='pdbsite=AC2:Cs7+Binding+Site+For+Residue+B+1'>AC2</scene>, <scene name='pdbsite=AC3:Tar+Binding+Site+For+Residue+A+448'>AC3</scene>, <scene name='pdbsite=AC4:Tar+Binding+Site+For+Residue+A+2'>AC4</scene> and <scene name='pdbsite=AC5:Tar+Binding+Site+For+Residue+B+3'>AC5</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CS7:'>CS7</scene> and <scene name='pdbligand=TAR:D(-)-TARTARIC ACID'>TAR</scene>
+<table><tr><td colspan='2'>[[2qmd]] 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=2QMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMD FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Memapsin_2 Memapsin 2], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.46 3.4.23.46]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</td></tr>
-|GENE= BACE1, BACE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CS7:N-[(1S,2R)-2-[(2R,4R)-4-(BENZYLOXY)PYRROLIDIN-2-YL]-1-(3,5-DIFLUOROBENZYL)-2-HYDROXYETHYL]-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE'>CS7</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</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=2qmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmd OCA], [https://pdbe.org/2qmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qmd RCSB], [https://www.ebi.ac.uk/pdbsum/2qmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qmd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BACE1_HUMAN BACE1_HUMAN] Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves at the N-terminus of the A-beta peptide sequence, between residues 671 and 672 of APP, leads to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase.<ref>PMID:10677483</ref> <ref>PMID:20354142</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qm/2qmd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qmd ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Based on lead compound 1 identified from the patent literature, we developed novel patentable BACE-1 inhibitors by introducing a cyclic amine scaffold. Extensive SAR studies on both pyrrolidines and piperidines ultimately led to inhibitor 2f, one of the most potent inhibitors synthesized to date.
-'''Structure of BACE Bound to SCH722924'''
+Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.,Iserloh U, Wu Y, Cumming JN, Pan J, Wang LY, Stamford AW, Kennedy ME, Kuvelkar R, Chen X, Parker EM, Strickland C, Voigt J Bioorg Med Chem Lett. 2008 Jan 1;18(1):414-7. Epub 2007 Nov 6. PMID:18023580<ref>PMID:18023580</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qmd" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Based on lead compound 1 identified from the patent literature, we developed novel patentable BACE-1 inhibitors by introducing a cyclic amine scaffold. Extensive SAR studies on both pyrrolidines and piperidines ultimately led to inhibitor 2f, one of the most potent inhibitors synthesized to date.
+*[[Beta secretase 3D structures|Beta secretase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-QMD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMD OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Potent pyrrolidine- and piperidine-based BACE-1 inhibitors., Iserloh U, Wu Y, Cumming JN, Pan J, Wang LY, Stamford AW, Kennedy ME, Kuvelkar R, Chen X, Parker EM, Strickland C, Voigt J, Bioorg Med Chem Lett. 2008 Jan 1;18(1):414-7. Epub 2007 Nov 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18023580 18023580]
 [[Category: Homo sapiens]]
-[[Category: Memapsin 2]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Iserloh U]]
-[[Category: Iserloh, U.]]
+[[Category: Strickland CO]]
-[[Category: Strickland, C O.]]
-[[Category: CS7]]
-[[Category: TAR]]
-[[Category: alternative splicing]]
-[[Category: aspartyl protease]]
-[[Category: bace1]]
-[[Category: glycoprotein]]
-[[Category: hydrolase]]
-[[Category: membrane]]
-[[Category: protease]]
-[[Category: transmembrane]]
-[[Category: zymogen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:27:19 2008''