3eq7: Difference between revisions

← Older edit Newer edit →

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{STRUCTURE_3eq7|  PDB=3eq7  |  SCENE=  }}
+==Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type inhibitors==
-===Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type inhibitors===
+<StructureSection load='3eq7' size='340' side='right' caption='[[3eq7]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
-{{ABSTRACT_PUBMED_19006380}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3eq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EQ7 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=X99:2-{3-[(2S)-4,4-DIFLUORO-2-(PYRROLIDIN-1-YLCARBONYL)PYRROLIDIN-1-YL]-3-OXOPROPYL}-ISOINDOLE-1,3(2H)-DIONE'>X99</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3eq8|3eq8]], [[3eq9|3eq9]]</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Prolyl_oligopeptidase Prolyl oligopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.26 3.4.21.26] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3eq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3eq7 RCSB], [http://www.ebi.ac.uk/pdbsum/3eq7 PDBsum]</span></td></tr>
+</table>
+== 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/eq/3eq7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Three novel, N-acyl-pro-pyrrolidine-type, inhibitors of prolyl oligopeptidase (POP) with nanomolar activities were synthesized and their binding analyzed to the host enzyme in the light of X-ray diffraction and molecular modeling studies. We were interested in the alteration in the binding affinity at the S3 site as a function of the properties of the N-terminal group of the inhibitors. Our studies revealed that, for inhibitors with flat aromatic terminal groups, the optimal length of the linker chain is three C-C bonds, but this increases to four C-C bonds if there is a bulky group in the terminal position. Molecular dynamics calculations indicate that this is due to the better fit into the binding pocket. A 4-fold enhancement of the inhibitor activity upon replacement of the 4-CH2 group of the proline ring by CF2 is a consequence of a weak hydrogen bond formed between the fluorine atom and the hydroxy group of Tyr473 of the host enzyme. There is notably good agreement between the calculated and experimental free energies of binding; the average error in the IC50 values is around 1 order of magnitude.
-==About this Structure==
+Prolyl oligopeptidase inhibition by N-acyl-pro-pyrrolidine-type molecules.,Kanai K, Aranyi P, Bocskei Z, Ferenczy G, Harmat V, Simon K, Batori S, Naray-Szabo G, Hermecz I J Med Chem. 2008 Dec 11;51(23):7514-22. PMID:19006380<ref>PMID:19006380</ref>
-[[3eq7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EQ7 OCA].
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
 ==See Also==
 *[[Prolyl Endopeptidase|Prolyl Endopeptidase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019006380</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Prolyl oligopeptidase]]
 [[Category: Sus scrofa]]
-[[Category: Aranyi, P.]]
+[[Category: Aranyi, P]]
-[[Category: Bocskei, Z.]]
+[[Category: Bocskei, Z]]
-[[Category: Ferenczy, G.]]
+[[Category: Ferenczy, G]]
-[[Category: Harmat, V.]]
+[[Category: Harmat, V]]
-[[Category: Hermecz, I.]]
+[[Category: Hermecz, I]]
-[[Category: Kanai, K.]]
+[[Category: Kanai, K]]
-[[Category: Naray-Szabo, G.]]
+[[Category: Naray-Szabo, G]]
-[[Category: Simon, K.]]
+[[Category: Simon, K]]
 [[Category: Hydrolase]]
 [[Category: Protease]]
 [[Category: Protease-inhibitor complex]]
 [[Category: Serine protease]]