6rd0: Difference between revisions

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

OCA

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-'''Unreleased structure'''
-The entry 6rd0 is ON HOLD  until Paper Publication
+==Human MMP12 catalytic domain in complex with AP280==
+<StructureSection load='6rd0' size='340' side='right'caption='[[6rd0]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6rd0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RD0 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=K0Q:~{N}-[2-(1~{H}-indol-3-yl)ethyl]-2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)ethanamide'>K0Q</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6rd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rd0 OCA], [https://pdbe.org/6rd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rd0 RCSB], [https://www.ebi.ac.uk/pdbsum/6rd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rd0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MMP12_HUMAN MMP12_HUMAN] May be involved in tissue injury and remodeling. Has significant elastolytic activity. Can accept large and small amino acids at the P1' site, but has a preference for leucine. Aromatic or hydrophobic residues are preferred at the P1 site, with small hydrophobic residues (preferably alanine) occupying P3.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The oxytocinase subfamily of M1 aminopeptidases consists of three members, ERAP1, ERAP2 and IRAP that play several important biological roles, including key functions in the generation of antigenic peptides that drive human immune responses. They represent emerging targets for pharmacological manipulation of the immune system, albeit lack of selective inhibitors is hampering these efforts. Most of the previously explored small-molecule binders target the active site of the enzymes via strong interactions with the catalytic zinc(II) atom and, while achieving increased potency, they suffer in selectivity. Continuing our earlier efforts on weaker zinc(II) binding groups (ZBG), like the 3,4-diaminobenzoic acid derivatives (DABA), we herein synthesized and biochemically evaluated analogues of nine potentially weak ZBGs, based on differential substitutions of functionalized pyridinone- and pyridinethione-scaffolds, nicotinic-, isonicotinic-, aminobenzoic- and hydrazinobenzoic-acids. Crystallographic analysis of two analogues in complex with a metalloprotease (MMP-12) revealed unexpected binding topologies, consistent with the observed affinities. Our results suggest that the potency of the compounds as inhibitors of ERAP1, ERAP2 and IRAP is primarily driven by the occupation of active-site specificity pockets and their proper orientation within the enzymes.
-Authors: Calderone, V., Fragai, M., Luchinat, C.
+Exploration of zinc-binding groups for the design of inhibitors for the oxytocinase subfamily of M1 aminopeptidases.,Tsoukalidou S, Kakou M, Mavridis I, Koumantou D, Calderone V, Fragai M, Stratikos E, Papakyriakou A, Vourloumis D Bioorg Med Chem. 2019 Dec 15;27(24):115177. doi: 10.1016/j.bmc.2019.115177. Epub , 2019 Nov 1. PMID:31711716<ref>PMID:31711716</ref>
-Description: Human MMP12 catalytic domain in complex with AP280
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Calderone, V]]
+<div class="pdbe-citations 6rd0" style="background-color:#fffaf0;"></div>
-[[Category: Fragai, M]]
-[[Category: Luchinat, C]]
+==See Also==
+*[[Matrix metalloproteinase 3D structures|Matrix metalloproteinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Calderone V]]
+[[Category: Fragai M]]
+[[Category: Luchinat C]]