3kej - Revision history

OCA at 08:45, 7 February 2024

OCA — Wed, 07 Feb 2024 08:45:13 GMT

←Older revision		Revision as of 08:45, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='3kej' size='340' side='right'caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3kej' size='340' side='right'caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3kec\|3kec]], [[3kek\|3kek]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [https://pdbe.org/3kej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [https://www.ebi.ac.uk/pdbsum/3kej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kej 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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [https://pdbe.org/3kej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [https://www.ebi.ac.uk/pdbsum/3kej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kej 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.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom. Compound 29b demonstrated reduction of cartilage degradation biomarker (TIINE) levels associated with cartilage protection in a preclinical rat osteoarthritis model.	+
-		+
-	Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.,Schnute ME, O'Brien PM, Nahra J, Morris M, Howard Roark W, Hanau CE, Ruminski PG, Scholten JA, Fletcher TR, Hamper BC, Carroll JN, Patt WC, Shieh HS, Collins B, Pavlovsky AG, Palmquist KE, Aston KW, Hitchcock J, Rogers MD, McDonald J, Johnson AR, Munie GE, Wittwer AJ, Man CF, Settle SL, Nemirovskiy O, Vickery LE, Agawal A, Dyer RD, Sunyer T Bioorg Med Chem Lett. 2010 Jan 15;20(2):576-80. Epub 2009 Nov 22. PMID:20005097<ref>PMID:20005097</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3kej" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
Line 29:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Collins, B]]	+	[[Category: Collins B]]
-	[[Category: Schnute~~, M E~~]]	+	[[Category: Schnute ME]]
-	[[Category: Shieh, H S]]	+	[[Category: Shieh H-S]]
-	~~[[Category: Collagen degradation]]~~	+
-	~~[[Category: Disease mutation]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Extracellular matrix]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Metalloprotease]]~~	+
-	~~[[Category: No contact to zn]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: S1' inhibitor]]~~	+
-	~~[[Category: S1' specificity pocket]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Selective mmp-13 inhibitor]]~~	+
-	~~[[Category: Zymogen~~]]	+

OCA at 13:34, 4 May 2022

OCA — Wed, 04 May 2022 13:34:49 GMT

←Older revision		Revision as of 13:34, 4 May 2022
Line 1:		Line 1:

	==Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound==		==Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound==
-	<StructureSection load='3kej' size='340' side='right' caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3kej' size='340' side='right'caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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">[[3kec\|3kec]], [[3kek\|3kek]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3kec\|3kec]], [[3kek\|3kek]]</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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [~~http~~://pdbe.org/3kej PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kej PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kej 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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [https://pdbe.org/3kej PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [https://www.ebi.ac.uk/pdbsum/3kej PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kej 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:

	==See Also==		==See Also==
-	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]	+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Collins, B]]		[[Category: Collins, B]]
	[[Category: Schnute, M E]]		[[Category: Schnute, M E]]

OCA at 09:17, 4 August 2016

OCA — Thu, 04 Aug 2016 09:17:37 GMT

←Older revision		Revision as of 09:17, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound==		==Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound==
	<StructureSection load='3kej' size='340' side='right' caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3kej' size='340' side='right' caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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">[[3kec\|3kec]], [[3kek\|3kek]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kec\|3kec]], [[3kek\|3kek]]</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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [http://www.ebi.ac.uk/pdbsum/3kej 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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [http://pdbe.org/3kej PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [http://www.ebi.ac.uk/pdbsum/3kej PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kej ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 21:
	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 3kej" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Collins, B]]		[[Category: Collins, B]]
	[[Category: Schnute, M E]]		[[Category: Schnute, M E]]

OCA at 16:18, 18 December 2014

OCA — Thu, 18 Dec 2014 16:18:19 GMT

←Older revision		Revision as of 16:18, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3kej\| PDB=3kej \| SCENE= }}~~	+	==Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound==
-	===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===	+	<StructureSection load='3kej' size='340' side='right' caption='[[3kej]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	{~~{ABSTRACT_PUBMED_20005097}~~}	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kej]] 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=3KEJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KEJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3EJ:4-[(5-{2-[(3-FLUOROBENZYL)CARBAMOYL]PYRIDIN-4-YL}-2H-TETRAZOL-2-YL)METHYL]BENZOIC+ACID'>3EJ</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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">[[3kec\|3kec]], [[3kek\|3kek]]</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=3kej FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kej OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kej RCSB], [http://www.ebi.ac.uk/pdbsum/3kej 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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Potent, highly selective and orally-bioavailable MMP-13 inhibitors have been identified based upon a (pyridin-4-yl)-2H-tetrazole scaffold. Co-crystal structure analysis revealed that the inhibitors bind at the S(1)(') active site pocket and are not ligands for the catalytic zinc atom. Compound 29b demonstrated reduction of cartilage degradation biomarker (TIINE) levels associated with cartilage protection in a preclinical rat osteoarthritis model.

-	~~==Disease==~~	+	Discovery of (pyridin-4-yl)-2H-tetrazole as a novel scaffold to identify highly selective matrix metalloproteinase-13 inhibitors for the treatment of osteoarthritis.,Schnute ME, O'Brien PM, Nahra J, Morris M, Howard Roark W, Hanau CE, Ruminski PG, Scholten JA, Fletcher TR, Hamper BC, Carroll JN, Patt WC, Shieh HS, Collins B, Pavlovsky AG, Palmquist KE, Aston KW, Hitchcock J, Rogers MD, McDonald J, Johnson AR, Munie GE, Wittwer AJ, Man CF, Settle SL, Nemirovskiy O, Vickery LE, Agawal A, Dyer RD, Sunyer T Bioorg Med Chem Lett. 2010 Jan 15;20(2):576-80. Epub 2009 Nov 22. PMID:20005097<ref>PMID:20005097</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==~~	+
-	~~[[3kej]] 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=3KEJ OCA].~~	+

	==See Also==		==See Also==
	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]		*[[Matrix metalloproteinase\|Matrix metalloproteinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020005097</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Collins, B.]]	+	[[Category: Collins, B]]
-	[[Category: Schnute, M E.]]	+	[[Category: Schnute, M E]]
-	[[Category: Shieh, H S.]]	+	[[Category: Shieh, H S]]
	[[Category: Collagen degradation]]		[[Category: Collagen degradation]]
	[[Category: Disease mutation]]		[[Category: Disease mutation]]

OCA at 11:30, 24 March 2013

OCA — Sun, 24 Mar 2013 11:30:04 GMT

←Older revision		Revision as of 11:30, 24 March 2013
Line 1:		Line 1:
-	[[Image:3kej.png\|left\|200px]]
-
	{{STRUCTURE_3kej\| PDB=3kej \| SCENE= }}		{{STRUCTURE_3kej\| PDB=3kej \| SCENE= }}
-
	===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===		===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===
		+	{{ABSTRACT_PUBMED_20005097}}

-	~~{{ABSTRACT_PUBMED_20005097}}~~	+	==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:020005097</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020005097</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Collins, B.]]		[[Category: Collins, B.]]

OCA at 05:41, 20 October 2012

OCA — Sat, 20 Oct 2012 05:41:37 GMT

←Older revision		Revision as of 05:41, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3kej]] 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=3KEJ OCA].	+	[[3kej]] 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=3KEJ OCA].

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

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

OCA — Wed, 25 Jul 2012 10:50:46 GMT

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

←Older revision

Revision as of 10:50, 25 July 2012

OCA at 10:50, 25 July 2012

OCA — Wed, 25 Jul 2012 10:50:44 GMT

←Older revision		Revision as of 10:50, 25 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3kej.png\|left\|200px]]
-	[[Image:3kej.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kej", 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_3kej\| PDB=3kej \| SCENE= }}		{{STRUCTURE_3kej\| PDB=3kej \| SCENE= }}

	===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===		===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20005097}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20005097 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20005097}}		{{ABSTRACT_PUBMED_20005097}}

	==About this Structure==		==About this Structure==
-	~~3KEJ~~ is a 2 ~~chains~~ structure with ~~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=3KEJ OCA].	+	[[3kej]] 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=3KEJ OCA].
		+
		+	==See Also==
		+	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20005097~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020005097</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Collins, B.]]		[[Category: Collins, B.]]
Line 44:		Line 35:
	[[Category: Selective mmp-13 inhibitor]]		[[Category: Selective mmp-13 inhibitor]]
	[[Category: Zymogen]]		[[Category: Zymogen]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:47:09 2010''

OCA at 03:36, 10 November 2010

OCA — Wed, 10 Nov 2010 03:36:14 GMT

←Older revision		Revision as of 03:36, 10 November 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kej.jpg\|left\|200px]]

-	The ~~entry 3kej~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kej", 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_3kej\| PDB=3kej \| SCENE= }}

-	~~Authors: Shieh, H.~~-~~S., Collins, B., Schnute, M.E.~~	+	===Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound===

-	Description: Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 7 08~~:24:41 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20005097}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20005097 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20005097}}
		+
		+	==About this Structure==
		+	3KEJ is a 2 chains structure with 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=3KEJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20005097</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Collins, B.]]
		+	[[Category: Schnute, M E.]]
		+	[[Category: Shieh, H S.]]
		+	[[Category: Collagen degradation]]
		+	[[Category: Disease mutation]]
		+	[[Category: Disulfide bond]]
		+	[[Category: Extracellular matrix]]
		+	[[Category: Glycoprotein]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Metal-binding]]
		+	[[Category: Metalloprotease]]
		+	[[Category: No contact to zn]]
		+	[[Category: Protease]]
		+	[[Category: S1' inhibitor]]
		+	[[Category: S1' specificity pocket]]
		+	[[Category: Secreted]]
		+	[[Category: Selective mmp-13 inhibitor]]
		+	[[Category: Zymogen]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 10 06:47:09 2010''

OCA at 04:18, 7 July 2010

OCA — Wed, 07 Jul 2010 04:18:49 GMT

←Older revision		Revision as of 04:18, 7 July 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3kej is ON HOLD ~~until sometime in the future~~	+	The entry 3kej is ON HOLD

-	Authors: Shieh, ~~Huey~~-~~Sheng~~, Collins, ~~Brandon~~, Schnute, ~~Mark~~ E.	+	Authors: Shieh, H.-S., Collins, B., Schnute, M.E.

	Description: Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound		Description: Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Nov 18 18~~:54:~~11 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 7 08:24:41 2010''