6ow2: Difference between revisions

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<StructureSection load='6ow2' size='340' side='right'caption='[[6ow2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
<StructureSection load='6ow2' size='340' side='right'caption='[[6ow2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6ow2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"diplococcus_pneumoniae"_(klein_1884)_weichselbaum_1886 "diplococcus pneumoniae" (klein 1884) weichselbaum 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OW2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OW2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6ow2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae Streptococcus pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OW2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OW2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NB4:(2R)-2-(cyclopentylmethyl)-N-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide'>NB4</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">defB, def, def_1, def_2, def_3, A5N45_09745, ERS019420_01538, ERS019688_00954, ERS020178_05158, ERS020534_01685, ERS020726_00048, ERS021057_00383, ERS021733_04069, ERS050646_01998, ERS367886_01588, ERS409327_03241, ERS409593_03947, KK0981_34260, NCTC12140_00964 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1313 "Diplococcus pneumoniae" (Klein 1884) Weichselbaum 1886])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NB4:(2R)-2-(cyclopentylmethyl)-N-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide'>NB4</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peptide_deformylase Peptide deformylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.88 3.5.1.88] </span></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=6ow2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ow2 OCA], [https://pdbe.org/6ow2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ow2 RCSB], [https://www.ebi.ac.uk/pdbsum/6ow2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ow2 ProSAT]</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=6ow2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ow2 OCA], [http://pdbe.org/6ow2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ow2 RCSB], [http://www.ebi.ac.uk/pdbsum/6ow2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ow2 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/Q939R9_STREE Q939R9_STREE]] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).[HAMAP-Rule:MF_00163]
[https://www.uniprot.org/uniprot/DEF_STRR6 DEF_STRR6] Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The discovery of a novel series of peptide deformylase inhibitors incorporating a piperazic acid amino acid found in nature is described. These compounds demonstrated potent in vitro enzymatic potency and antimicrobial activity. Crystal structure analysis revealed the piperazic acid optimized a key contact with the PDF protein that accounted for the increased enzymatic potency of these compounds. We describe lead optimization of the P3' region of the series that resulted in a compound with good potency against three target organisms. One molecule showed in vivo efficacy in a rat respiratory infection model but ultimately did not meet candidate progression criteria.
 
Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.,Spletstoser JT, Dreabit J, Knox AN, Benowitz A, Campobasso N, Ward P, Cui G, Lewandowski T, McCloskey L, Aubart KM Bioorg Med Chem Lett. 2019 May 16. pii: S0960-894X(19)30325-7. doi:, 10.1016/j.bmcl.2019.05.028. PMID:31160176<ref>PMID:31160176</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6ow2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Peptide deformylase]]
[[Category: Streptococcus pneumoniae]]
[[Category: Campobasso, N]]
[[Category: Campobasso N]]
[[Category: Spletstoser, J]]
[[Category: Spletstoser J]]
[[Category: Ward, P]]
[[Category: Ward P]]
[[Category: Complex]]
[[Category: Enzyme]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Inhibitor]]
[[Category: Metal protein]]

Latest revision as of 14:53, 13 March 2024

X-ray Structure of Polypeptide Deformylase

6ow2, resolution 1.70Å

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