3i7g - Revision history

OCA at 10:04, 21 February 2024

2024-02-21T10:04:15Z

←Older revision		Revision as of 10:04, 21 February 2024
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	<StructureSection load='3i7g' size='340' side='right'caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7g' size='340' side='right'caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7g]] is a 2 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=3I7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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]] 1.95Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i7i\|3i7i]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">MMP13 ([https://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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [https://pdbe.org/3i7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [https://www.ebi.ac.uk/pdbsum/3i7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7g 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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [https://pdbe.org/3i7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [https://www.ebi.ac.uk/pdbsum/3i7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7g ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[https://omim.org/entry/602111 602111]]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[https://omim.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>	+	[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[https://omim.org/entry/602111 602111]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[https://omim.org/entry/602111 602111]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.	+	[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i7g ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i7g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1' pocket.
-
-	Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors.,Heim-Riether A, Taylor SJ, Liang S, Gao DA, Xiong Z, Michael August E, Collins BK, Farmer BT 2nd, Haverty K, Hill-Drzewi M, Junker HD, Mariana Margarit S, Moss N, Neumann T, Proudfoot JR, Keenan LS, Sekul R, Zhang Q, Li J, Farrow NA Bioorg Med Chem Lett. 2009 Sep 15;19(18):5321-4. Epub 2009 Aug 3. PMID:19692239<ref>PMID:19692239</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3i7g" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Farrow~~, N A]]~~	+	[[Category: Farrow NA]]
-	~~[[Category: Calcium]]~~	+
-	~~[[Category: Collagen degradation]]~~	+
-	~~[[Category: Disease mutation]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Extracellular matrix]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Metalloprotease]]~~	+
-	~~[[Category: Polymorphism]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zymogen~~]]	+

OCA at 10:59, 13 April 2022

2022-04-13T10:59:56Z

←Older revision		Revision as of 10:59, 13 April 2022
Line 1:		Line 1:

	==MMP-13 in complex with a non zinc-chelating inhibitor==		==MMP-13 in complex with a non zinc-chelating inhibitor==
-	<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3i7g' size='340' side='right'caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7g]] is a 2 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=3I7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3I7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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" id="ligandDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">[[3i7i\|3i7i]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3i7i\|3i7i]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [~~http~~://pdbe.org/3i7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3i7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7g 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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [https://pdbe.org/3i7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [https://www.ebi.ac.uk/pdbsum/3i7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7g ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[~~http~~://omim.org/entry/602111 602111]]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[~~http~~://omim.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>	+	[[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[https://omim.org/entry/602111 602111]]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[https://omim.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.	+	[[https://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]	+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 40:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Farrow, N A]]		[[Category: Farrow, N A]]
	[[Category: Calcium]]		[[Category: Calcium]]

OCA at 09:28, 19 December 2018

2018-12-19T09:28:20Z

←Older revision		Revision as of 09:28, 19 December 2018
Line 1:		Line 1:
		+
	==MMP-13 in complex with a non zinc-chelating inhibitor==		==MMP-13 in complex with a non zinc-chelating inhibitor==
	<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7i\|3i7i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7i\|3i7i]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [http://pdbe.org/3i7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [http://www.ebi.ac.uk/pdbsum/3i7g PDBsum]</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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [http://pdbe.org/3i7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [http://www.ebi.ac.uk/pdbsum/3i7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3i7g ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7g_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7g_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 40:		Line 41:
	[[Category: Human]]		[[Category: Human]]
	[[Category: Farrow, N A]]		[[Category: Farrow, N A]]
		+	[[Category: Calcium]]
	[[Category: Collagen degradation]]		[[Category: Collagen degradation]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
Line 48:		Line 50:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Metalloprotease]]		[[Category: Metalloprotease]]
		+	[[Category: Polymorphism]]
	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Secreted]]		[[Category: Secreted]]
		+	[[Category: Zinc]]
	[[Category: Zymogen]]		[[Category: Zymogen]]

OCA at 16:32, 9 February 2016

2016-02-09T16:32:00Z

←Older revision		Revision as of 16:32, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3i7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3i7g]] is a 2 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=3I7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">[[3i7i\|3i7i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3i7i\|3i7i]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [http://www.ebi.ac.uk/pdbsum/3i7g PDBsum]</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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [http://pdbe.org/3i7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [http://www.ebi.ac.uk/pdbsum/3i7g PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i7g ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3i7g" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Farrow, N A]]		[[Category: Farrow, N A]]
	[[Category: Collagen degradation]]		[[Category: Collagen degradation]]

OCA at 16:43, 18 December 2014

2014-12-18T16:43:21Z

←Older revision		Revision as of 16:43, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}~~	+	==MMP-13 in complex with a non zinc-chelating inhibitor==
-	===MMP-13 in complex with a non zinc-chelating inhibitor===	+	<StructureSection load='3i7g' size='340' side='right' caption='[[3i7g]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19692239}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3i7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3I7G FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=732:5-(4-CHLOROPHENYL)-N-[(1S)-1-CYCLOHEXYL-2-(METHYLAMINO)-2-OXOETHYL]FURAN-2-CARBOXAMIDE'>732</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</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">[[3i7i\|3i7i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MMP13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3i7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i7g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3i7g RCSB], [http://www.ebi.ac.uk/pdbsum/3i7g PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[http://omim.org/entry/602111 602111]]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[http://omim.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i7/3i7g_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Discovery and optimization of potency and selectivity of a non-Zn-chelating MMP-13 inhibitor with the aid of protein co-crystal structural information is reported. This inhibitor was observed to have a binding mode distinct from previously published MMP-13 inhibitors. Potency and selectivity were improved by extending the hit structure out from the active site into the S1' pocket.

-	~~==Disease==~~	+	Improving potency and selectivity of a new class of non-Zn-chelating MMP-13 inhibitors.,Heim-Riether A, Taylor SJ, Liang S, Gao DA, Xiong Z, Michael August E, Collins BK, Farmer BT 2nd, Haverty K, Hill-Drzewi M, Junker HD, Mariana Margarit S, Moss N, Neumann T, Proudfoot JR, Keenan LS, Sekul R, Zhang Q, Li J, Farrow NA Bioorg Med Chem Lett. 2009 Sep 15;19(18):5321-4. Epub 2009 Aug 3. PMID:19692239<ref>PMID:19692239</ref>
-	~~[[http://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause~~ of ~~spondyloepimetaphyseal dysplasia Missouri type (SEMD~~-~~MO) [MIM:[http://omim.org/entry/602111 602111]]~~. A ~~bone disease characterized by moderate to severe metaphyseal changes~~, ~~mild epiphyseal involvement~~, ~~rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae~~, ~~coxa vara~~, ~~genu varum and pear~~-~~shaped vertebrae in childhood~~. ~~Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1~~ (~~MANDP1~~) ~~[MIM~~:~~[http://omim~~.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:~~19615667~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www~~.~~uniprot~~.~~org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process~~.	+	</div>
-		+
-	~~==About this Structure==~~	+
-	~~[[3i7g]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].~~	+

	==See Also==		==See Also==
	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]		*[[Matrix metalloproteinase\|Matrix metalloproteinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019692239</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Farrow, N A.]]	+	[[Category: Farrow, N A]]
	[[Category: Collagen degradation]]		[[Category: Collagen degradation]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]

OCA at 12:15, 24 March 2013

2013-03-24T12:15:08Z

←Older revision		Revision as of 12:15, 24 March 2013
Line 1:		Line 1:
-	[[Image:3i7g.png\|left\|200px]]
-
	{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}		{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}
-
	===MMP-13 in complex with a non zinc-chelating inhibitor===		===MMP-13 in complex with a non zinc-chelating inhibitor===
		+	{{ABSTRACT_PUBMED_19692239}}

-	~~{{ABSTRACT_PUBMED_19692239}}~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:[http://omim.org/entry/602111 602111]]. A bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae in childhood. Epimetaphyseal changes improve with age.<ref>PMID:16167086</ref> Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:[http://omim.org/entry/602111 602111]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.<ref>PMID:19615667</ref>
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/MMP13_HUMAN MMP13_HUMAN]] Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process.

	==About this Structure==		==About this Structure==
Line 14:		Line 16:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019692239</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019692239</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Farrow, N A.]]		[[Category: Farrow, N A.]]

OCA at 14:27, 20 October 2012

2012-10-20T14:27:47Z

←Older revision		Revision as of 14:27, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3i7g]] is a 2 chain structure ~~of [[Matrix metalloproteinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].	+	[[3i7g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].

	==See Also==		==See Also==

OCA: Protected "3i7g" [edit=sysop:move=sysop]

2012-07-26T15:13:08Z

Protected "3i7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:13, 26 July 2012

OCA at 15:13, 26 July 2012

2012-07-26T15:13:05Z

←Older revision		Revision as of 15:13, 26 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3i7g.png\|left\|200px]]
-	[[Image:3i7g.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3i7g", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}		{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}

	===MMP-13 in complex with a non zinc-chelating inhibitor===		===MMP-13 in complex with a non zinc-chelating inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19692239}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19692239 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19692239}}		{{ABSTRACT_PUBMED_19692239}}

	==About this Structure==		==About this Structure==
-	~~3I7G~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].	+	[[3i7g]] is a 2 chain structure of [[Matrix metalloproteinase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].
		+
		+	==See Also==
		+	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19692239~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019692239</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Farrow, N A.]]		[[Category: Farrow, N A.]]
-	[[Category: Calcium]]
	[[Category: Collagen degradation]]		[[Category: Collagen degradation]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]
Line 35:		Line 25:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Metalloprotease]]		[[Category: Metalloprotease]]
-	[[Category: Polymorphism]]
	[[Category: Protease]]		[[Category: Protease]]
	[[Category: Secreted]]		[[Category: Secreted]]
-	[[Category: Zinc]]
	[[Category: Zymogen]]		[[Category: Zymogen]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:01:25 2009''

OCA at 13:01, 3 September 2009

2009-09-03T13:01:32Z

←Older revision		Revision as of 13:01, 3 September 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3i7g.jpg\|left\|200px]]

-	The ~~entry 3i7g~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3i7g", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3i7g\| PDB=3i7g \| SCENE= }}

-	~~Authors: Farrow, N.A.~~	+	===MMP-13 in complex with a non zinc-chelating inhibitor===

-	Description: MMP-13 in complex with a non zinc-chelating inhibitor

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 15 08~~:30:45 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19692239}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19692239 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19692239}}
		+
		+	==About this Structure==
		+	3I7G is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I7G OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19692239</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Farrow, N A.]]
		+	[[Category: Calcium]]
		+	[[Category: Collagen degradation]]
		+	[[Category: Disease mutation]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Extracellular matrix]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Metalloprotease]]
		+	[[Category: Polymorphism]]
		+	[[Category: Protease]]
		+	[[Category: Secreted]]
		+	[[Category: Zinc]]
		+	[[Category: Zymogen]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Sep 3 16:01:25 2009''