3dp1: Difference between revisions

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-{{Seed}}
-[[Image:3dp1.jpg|left|200px]]
-<!--
+==Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3n==
-The line below this paragraph, containing "STRUCTURE_3dp1", creates the "Structure Box" on the page.
+<StructureSection load='3dp1' size='340' side='right'caption='[[3dp1]], [[Resolution|resolution]] 2.30&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'>[[3dp1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DP1 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2RB:N-[(1E)-(3,5-DIBROMO-2,4-DIHYDROXYPHENYL)METHYLIDENE]-4-METHOXYBENZOHYDRAZIDE'>2RB</scene>, <scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_3dp1|  PDB=3dp1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dp1 OCA], [https://pdbe.org/3dp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dp1 RCSB], [https://www.ebi.ac.uk/pdbsum/3dp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dp1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5G940_HELPX Q5G940_HELPX] Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs.[HAMAP-Rule:MF_00406]  Involved in unsaturated fatty acids biosynthesis. Catalyzes the dehydration of short chain beta-hydroxyacyl-ACPs and long chain saturated and unsaturated beta-hydroxyacyl-ACPs (By similarity).[SAAS:SAAS00205551]
+== 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/dp/3dp1_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/main_output.php?pdb_ID=3dp1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The discovery of HpFabZ inhibitors is now of special interest in the treatment of various gastric diseases. In this work, three series of derivatives (compounds 3, 4, and 5) were designed, synthesized, and their biological activities were investigated as potential HpFabZ inhibitors in a two phased manner. First, we designed and synthesized two series of derivatives (3a-r and 4a-u) and evaluated the enzyme-based assay against HpFabZ. Five compounds (3i-k, 3m, and 3q) showed potential inhibitory activity, with IC(50) values less than 2 muM. Second, a focused combinatorial library containing 280 molecules was designed employing the LD1.0 program. Twelve compounds (5a-l) were selected and synthesized. The activity of the most potent compound 5h (IC(50) = 0.86 muM) was 46 times higher than that of the hit 1. The high hit rate and the potency of the new HpFabZ inhibitors demonstrated the efficiency of the strategy for the focused library design and virtual screening.
-===Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from Helicobacter pylori in complex with compound 3n===
+Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination.,He L, Zhang L, Liu X, Li X, Zheng M, Li H, Yu K, Chen K, Shen X, Jiang H, Liu H J Med Chem. 2009 Apr 23;52(8):2465-81. PMID:19309082<ref>PMID:19309082</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dp1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19309082}}, adds the Publication Abstract to the page
+*[[Beta-hydroxyacyl-acyl carrier protein dehydratase 3D structures|Beta-hydroxyacyl-acyl carrier protein dehydratase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19309082 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19309082}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DP1 is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DP1 OCA].
-==Reference==
-<ref group="xtra">PMID:19309082</ref><references group="xtra"/>
 [[Category: Helicobacter pylori]]
-[[Category: He, L.]]
+[[Category: Large Structures]]
-[[Category: Jiang, H.]]
+[[Category: He L]]
-[[Category: Liu, H.]]
+[[Category: Jiang H]]
-[[Category: Liu, X.]]
+[[Category: Liu H]]
-[[Category: Shen, X.]]
+[[Category: Liu X]]
-[[Category: Zhang, L.]]
+[[Category: Shen X]]
-[[Category: Fabz complex]]
+[[Category: Zhang L]]
-[[Category: Lyase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  6 10:22:27 2009''