6rly - Revision history

OCA at 12:23, 24 January 2024

2024-01-24T12:23:22Z

←Older revision		Revision as of 12:23, 24 January 2024
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	<StructureSection load='6rly' size='340' side='right'caption='[[6rly]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6rly' size='340' side='right'caption='[[6rly]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rly]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RLY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RLY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rly]] 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=6RLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RLY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=K8T:2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide'>K8T</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.2Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Macrophage_elastase Macrophage elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.65 3.4.24.65] </span></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=K8T:2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide'>K8T</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6rly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rly OCA], [~~http~~://pdbe.org/6rly PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6rly RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6rly PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6rly ProSAT]</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=6rly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rly OCA], [https://pdbe.org/6rly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rly RCSB], [https://www.ebi.ac.uk/pdbsum/6rly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rly ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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.	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6rly" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6rly" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Macrophage elastase]]~~	+	[[Category: Calderone V]]
-	[[Category: Calderone, V]]	+	[[Category: Fragai M]]
-	[[Category: Fragai, M]]	+	[[Category: Luchinat C]]
-	[[Category: Luchinat, C]]	+
-	~~[[Category: Catalytic domain]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Mmp12~~]]	+

OCA at 07:25, 11 March 2020

2020-03-11T07:25:55Z

←Older revision		Revision as of 07:25, 11 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rly is ~~ON HOLD~~	+	==Human MMP12 (catalytic domain) in complex with AP316==
		+	<StructureSection load='6rly' size='340' side='right'caption='[[6rly]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6rly]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RLY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HAE:ACETOHYDROXAMIC+ACID'>HAE</scene>, <scene name='pdbligand=K8T:2-(3-oxidanyl-2-oxidanylidene-pyridin-1-yl)-~{N}-[2-(4-phenylphenyl)ethyl]ethanamide'>K8T</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Macrophage_elastase Macrophage elastase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.65 3.4.24.65] </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=6rly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rly OCA], [http://pdbe.org/6rly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rly RCSB], [http://www.ebi.ac.uk/pdbsum/6rly PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rly ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 AP316~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Luchinat, C~~]]	+	<div class="pdbe-citations 6rly" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Macrophage elastase]]
	[[Category: Calderone, V]]		[[Category: Calderone, V]]
	[[Category: Fragai, M]]		[[Category: Fragai, M]]
		+	[[Category: Luchinat, C]]
		+	[[Category: Catalytic domain]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Mmp12]]

OCA: Protected "6rly" [edit=sysop:move=sysop]

2019-05-10T08:34:19Z

Protected "6rly" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:34, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6rly is ON HOLD Authors: Calderone, V., Fragai, M., Luchinat, C. Description: Human MMP12 (catalytic domain) in complex with AP316 [[Category: Unre...

2019-05-10T08:34:16Z

New page: '''Unreleased structure''' The entry 6rly is ON HOLD Authors: Calderone, V., Fragai, M., Luchinat, C. Description: Human MMP12 (catalytic domain) in complex with AP316 [[Category: Unre...

New page

'''Unreleased structure'''

The entry 6rly is ON HOLD

Authors: Calderone, V., Fragai, M., Luchinat, C.

Description: Human MMP12 (catalytic domain) in complex with AP316
[[Category: Unreleased Structures]]
[[Category: Luchinat, C]]
[[Category: Calderone, V]]
[[Category: Fragai, M]]