4d9p: Difference between revisions

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-[[Image:4d9p.png|left|200px]]
-{{STRUCTURE_4d9p|  PDB=4d9p  |  SCENE=  }}
+==Crystal structure of B. anthracis DHPS with compound 17==
+<StructureSection load='4d9p' size='340' side='right' caption='[[4d9p]], [[Resolution|resolution]] 2.26&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4d9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis_a2012 Bacillus anthracis a2012]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4D9P FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=Z17:(3R)-3-(7-AMINO-1-METHYL-4,5-DIOXO-1,4,5,6-TETRAHYDROPYRIMIDO[4,5-C]PYRIDAZIN-3-YL)BUTANOIC+ACID'>Z17</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tws|1tws]], [[4d8a|4d8a]], [[4d8z|4d8z]], [[4daf|4daf]], [[4dai|4dai]], [[4db7|4db7]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">folP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=191218 Bacillus anthracis A2012])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydropteroate_synthase Dihydropteroate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.15 2.5.1.15] </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=4d9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9p OCA], [http://pdbe.org/4d9p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4d9p RCSB], [http://www.ebi.ac.uk/pdbsum/4d9p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/C3P9L8_BACAA C3P9L8_BACAA]] DHPS catalyzes the formation of the immediate precursor of folic acid.[RuleBase:RU361205]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Dihydropteroate synthase (DHPS) is the validated drug target for sulfonamide antimicrobial therapy. However, due to widespread drug resistance and poor tolerance, the use of sulfonamide antibiotics is now limited. The pterin binding pocket in DHPS is highly conserved and is distinct from the sulfonamide binding site. It therefore represents an attractive alternative target for the design of novel antibacterial agents. We previously carried out the structural characterization of a known pyridazine inhibitor in the Bacillus anthracis DHPS pterin site and identified a number of unfavorable interactions that appear to compromise binding. With this structural information, a series of 4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazines were designed to improve binding affinity. Most importantly, the N-methyl ring substitution was removed to improve binding within the pterin pocket, and the length of the side chain carboxylic acid was optimized to fully engage the pyrophosphate binding site. These inhibitors were synthesized and evaluated by an enzyme activity assay, X-ray crystallography, isothermal calorimetry, and surface plasmon resonance to obtain a comprehensive understanding of the binding interactions from structural, kinetic, and thermodynamic perspectives. This study clearly demonstrates that compounds lacking the N-methyl substitution exhibit increased inhibition of DHPS, but the beneficial effects of optimizing the side chain length are less apparent.
-===Crystal structure of B. anthracis DHPS with compound 17===
+Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity.,Zhao Y, Hammoudeh D, Yun MK, Qi J, White SW, Lee RE ChemMedChem. 2012 Mar 13. doi: 10.1002/cmdc.201200049. PMID:22416048<ref>PMID:22416048</ref>
-{{ABSTRACT_PUBMED_22416048}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 4d9p" style="background-color:#fffaf0;"></div>
-[[4d9p]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_anthracis Bacillus anthracis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9P OCA].
 ==See Also==
 *[[Dihydropteroate synthase|Dihydropteroate synthase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:022416048</ref><references group="xtra"/>
+__TOC__
-[[Category: Bacillus anthracis]]
+</StructureSection>
+[[Category: Bacillus anthracis a2012]]
 [[Category: Dihydropteroate synthase]]
-[[Category: Hammoudeh, D.]]
+[[Category: Hammoudeh, D]]
-[[Category: Lee, R E.]]
+[[Category: Lee, R E]]
-[[Category: White, S W.]]
+[[Category: White, S W]]
 [[Category: Dhpp]]
 [[Category: Dhps inhibitor]]