5i4o - Revision history

OCA at 08:23, 23 August 2023

OCA — Wed, 23 Aug 2023 08:23:07 GMT

←Older revision		Revision as of 08:23, 23 August 2023
Line 1:		Line 1:

	==Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).==		==Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).==
-	<StructureSection load='5i4o' size='340' side='right' caption='[[5i4o]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5i4o' size='340' side='right'caption='[[5i4o]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i4o]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I4O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5I4O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i4o]] is a 4 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=5I4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I4O 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=V28:N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1-BIPHENYL]-4-YL)SULFONYL]-D-VALINE'>V28</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]] 2.05Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3m\|5i3m]], [[5i2z\|5i2z]], [[5iol\|5iol]], [[5i43\|5i43]], [[5i12\|5i12]]</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=V28:N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1-BIPHENYL]-4-YL)SULFONYL]-D-VALINE'>V28</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP12, HME ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4o OCA], [https://pdbe.org/5i4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i4o RCSB], [https://www.ebi.ac.uk/pdbsum/5i4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4o ProSAT]</span></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=5i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4o OCA], [~~http~~://pdbe.org/5i4o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5i4o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5i4o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4o 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 ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5i4o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5i4o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Macrophage elastase~~]]	+	[[Category: Large Structures]]
-	[[Category: Ciccone, L]]	+	[[Category: Ciccone L]]
-	[[Category: Cuffaro, D]]	+	[[Category: Cuffaro D]]
-	[[Category: Rosalia, L]]	+	[[Category: Rosalia L]]
-	[[Category: Rossello, A]]	+	[[Category: Rossello A]]
-	[[Category: Stura~~, E A~~]]	+	[[Category: Stura EA]]
-	[[Category: Tepshi, L]]	+	[[Category: Tepshi L]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Glycoconjugate]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Metalloprotease~~]]	+

OCA at 20:35, 24 January 2018

OCA — Wed, 24 Jan 2018 20:35:50 GMT

←Older revision		Revision as of 20:35, 24 January 2018
Line 3:		Line 3:
	<StructureSection load='5i4o' size='340' side='right' caption='[[5i4o]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5i4o' size='340' side='right' caption='[[5i4o]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5i4o]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5i4o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4O 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=V28:N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1-BIPHENYL]-4-YL)SULFONYL]-D-VALINE'>V28</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</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=V28:N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1-BIPHENYL]-4-YL)SULFONYL]-D-VALINE'>V28</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3m\|5i3m]], [[5i2z\|5i2z]], [[5iol\|5iol]], [[5i43\|5i43]], [[5i12\|5i12]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3m\|5i3m]], [[5i2z\|5i2z]], [[5iol\|5iol]], [[5i43\|5i43]], [[5i12\|5i12]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP12, HME ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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='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=5i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4o OCA], [http://pdbe.org/5i4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i4o RCSB], [http://www.ebi.ac.uk/pdbsum/5i4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4o 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=5i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4o OCA], [http://pdbe.org/5i4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i4o RCSB], [http://www.ebi.ac.uk/pdbsum/5i4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4o ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Macrophage elastase]]		[[Category: Macrophage elastase]]
	[[Category: Ciccone, L]]		[[Category: Ciccone, L]]

OCA at 18:01, 13 July 2016

OCA — Wed, 13 Jul 2016 18:01:36 GMT

←Older revision		Revision as of 18:01, 13 July 2016
Line 11:		Line 11:
	== 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.		[[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 ==
		+	Matrix metalloproteinase-12 (MMP-12) can be considered an attractive target to study selective inhibitors useful in the development of new therapies for lung and cardiovascular diseases. In this study, a new series of arylsulfonamide carboxylates, with increased hydrophilicity resulting from conjugation with a beta-N-acetyl-d-glucosamine moiety, were designed and synthesized as MMP-12 selective inhibitors. Their inhibitory activity was evaluated on human MMPs by using the fluorimetric assay, and a crystallographic analysis was performed to characterize their binding mode. Among these glycoconjugates, a nanomolar MMP-12 inhibitor with improved water solubility, compound 3 [(R)-2-(N-(2-(3-(2-acetamido-2-deoxy-beta-d-glucopyranosyl)thioureido)ethyl)biphe nyl-4-ylsulfonamido)-3-methylbutanoic acid], was identified.
		+
		+	Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors.,Nuti E, Cuffaro D, D'Andrea F, Rosalia L, Tepshi L, Fabbi M, Carbotti G, Ferrini S, Santamaria S, Camodeca C, Ciccone L, Orlandini E, Nencetti S, Stura EA, Dive V, Rossello A ChemMedChem. 2016 Jun 30. doi: 10.1002/cmdc.201600235. PMID:27356908<ref>PMID:27356908</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5i4o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 02:59, 13 July 2016

OCA — Wed, 13 Jul 2016 02:59:18 GMT

←Older revision		Revision as of 02:59, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5i4o is ON HOLD~~	+	==Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).==
-		+	<StructureSection load='5i4o' size='340' side='right' caption='[[5i4o]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L., Ciccone, L., Rossello, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5i4o]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I4O FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).	+	</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=V28:N-({1-[2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-N-[([1,1-BIPHENYL]-4-YL)SULFONYL]-D-VALINE'>V28</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5i3m\|5i3m]], [[5i2z\|5i2z]], [[5iol\|5iol]], [[5i43\|5i43]], [[5i12\|5i12]]</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=5i4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i4o OCA], [http://pdbe.org/5i4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i4o RCSB], [http://www.ebi.ac.uk/pdbsum/5i4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i4o 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.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Macrophage elastase]]
		+	[[Category: Ciccone, L]]
		+	[[Category: Cuffaro, D]]
		+	[[Category: Rosalia, L]]
	[[Category: Rossello, A]]		[[Category: Rossello, A]]
-	[[Category: Stura, E.A]]	+	[[Category: Stura, E A]]
-	~~[[Category: Ciccone, L~~]]	+
	[[Category: Tepshi, L]]		[[Category: Tepshi, L]]
-	[[Category: ~~Rosalia, L~~]]	+	[[Category: Complex]]
-	[[Category: ~~Cuffaro, D~~]]	+	[[Category: Glycoconjugate]]
		+	[[Category: Hydrolase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Metalloprotease]]

OCA at 00:12, 11 May 2016

OCA — Wed, 11 May 2016 00:12:15 GMT

←Older revision		Revision as of 00:12, 11 May 2016
Line 3:		Line 3:
	The entry 5i4o is ON HOLD		The entry 5i4o is ON HOLD

-	Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L.., Ciccone, L., Rossello, A.	+	Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L., Ciccone, L., Rossello, A.

	Description: Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).		Description: Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).

OCA: Protected "5i4o" [edit=sysop:move=sysop]

OCA — Fri, 26 Feb 2016 16:45:51 GMT

Protected "5i4o" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:45, 26 February 2016

OCA: New page: '''Unreleased structure''' The entry 5i4o is ON HOLD Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L.., Ciccone, L., Rossello, A. Description: Crystal structure of the cataly...

OCA — Fri, 26 Feb 2016 16:45:50 GMT

New page: '''Unreleased structure''' The entry 5i4o is ON HOLD Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L.., Ciccone, L., Rossello, A. Description: Crystal structure of the cataly...

New page

'''Unreleased structure'''

The entry 5i4o is ON HOLD

Authors: Stura, E.A., Rosalia, L., Cuffaro, D., Tepshi, L.., Ciccone, L., Rossello, A.

Description: Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28).
[[Category: Unreleased Structures]]
[[Category: Rossello, A]]
[[Category: Stura, E.A]]
[[Category: Ciccone, L]]
[[Category: Tepshi, L]]
[[Category: Rosalia, L]]
[[Category: Cuffaro, D]]