3pww: Difference between revisions

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-[[Image:3pww.png|left|200px]]
-<!--
+==Endothiapepsin in complex with saquinavir==
-The line below this paragraph, containing "STRUCTURE_3pww", creates the "Structure Box" on the page.
+<StructureSection load='3pww' size='340' side='right'caption='[[3pww]], [[Resolution|resolution]] 1.22&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3pww]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PWW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PWW FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.22&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ROC:(2S)-N-[(2S,3R)-4-[(2S,3S,4AS,8AS)-3-(TERT-BUTYLCARBAMOYL)-3,4,4A,5,6,7,8,8A-OCTAHYDRO-1H-ISOQUINOLIN-2-YL]-3-HYDROXY-1-PHENYL-BUTAN-2-YL]-2-(QUINOLIN-2-YLCARBONYLAMINO)BUTANEDIAMIDE'>ROC</scene></td></tr>
-{{STRUCTURE_3pww|  PDB=3pww  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pww FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pww OCA], [https://pdbe.org/3pww PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pww RCSB], [https://www.ebi.ac.uk/pdbsum/3pww PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pww ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CARP_CRYPA CARP_CRYPA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.
-===Endothiapepsin in complex with saquinavir===
+Experimental and Computational Active Site Mapping as a Starting Point to Fragment-Based Lead Discovery.,Behnen J, Koster H, Neudert G, Craan T, Heine A, Klebe G ChemMedChem. 2011 Dec 23. doi: 10.1002/cmdc.201100490. PMID:22213702<ref>PMID:22213702</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3pww" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22213702}}, adds the Publication Abstract to the page
+*[[Pepsin|Pepsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22213702 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22213702}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3pww]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cryphonectria_parasitica Cryphonectria parasitica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PWW OCA].
-==Reference==
-<ref group="xtra">PMID:022213702</ref><references group="xtra"/>
 [[Category: Cryphonectria parasitica]]
-[[Category: Endothiapepsin]]
+[[Category: Large Structures]]
-[[Category: Heine, A.]]
+[[Category: Heine A]]
-[[Category: Klebe, G.]]
+[[Category: Klebe G]]
-[[Category: Koester, H.]]
+[[Category: Koester H]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]