5gmn - Revision history

OCA at 11:36, 2 August 2023

OCA — Wed, 02 Aug 2023 11:36:33 GMT

←Older revision		Revision as of 11:36, 2 August 2023
Line 1:		Line 1:

	==Crystal structure of human carbonic anhydrase II in complex with polmacoxib==		==Crystal structure of human carbonic anhydrase II in complex with polmacoxib==
-	<StructureSection load='5gmn' size='340' side='right' caption='[[5gmn]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='5gmn' size='340' side='right'caption='[[5gmn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmn]] is a 1 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=5GMN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GMN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=949:4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE-FURAN-2-YL]BENZENESULFONAMIDE'>949</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]] 1.8Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5gmm\|5gmm~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=949:4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE-FURAN-2-YL]BENZENESULFONAMIDE'>949</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"~~>CA2 ([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=5gmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmn OCA], [https://pdbe.org/5gmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gmn RCSB], [https://www.ebi.ac.uk/pdbsum/5gmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmn 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/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1]~~ </~~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=5gmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmn OCA], [~~http~~://pdbe.org/5gmn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gmn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gmn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[~~http~~://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[https://omim.org/entry/259730 259730]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>	+	[https://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 23:

	==See Also==		==See Also==
-	*[[Carbonic anhydrase\|Carbonic anhydrase]]	+	*[[Carbonic anhydrase 3D structures\|Carbonic anhydrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carbonate dehydratase~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Hwang~~, K Y~~]]	+	[[Category: Hwang KY]]
-	[[Category: Kim~~, H T]]~~	+	[[Category: Kim HT]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:16, 20 June 2018

OCA — Wed, 20 Jun 2018 06:16:27 GMT

←Older revision		Revision as of 06:16, 20 June 2018
Line 3:		Line 3:
	<StructureSection load='5gmn' size='340' side='right' caption='[[5gmn]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='5gmn' size='340' side='right' caption='[[5gmn]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gmn]] is a 1 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=5GMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=949:4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE-FURAN-2-YL]BENZENESULFONAMIDE'>949</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=949:4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE-FURAN-2-YL]BENZENESULFONAMIDE'>949</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">[[5gmm\|5gmm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5gmm\|5gmm]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CA2 ([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/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </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=5gmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmn OCA], [http://pdbe.org/5gmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmn RCSB], [http://www.ebi.ac.uk/pdbsum/5gmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmn 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=5gmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmn OCA], [http://pdbe.org/5gmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmn RCSB], [http://www.ebi.ac.uk/pdbsum/5gmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmn ProSAT]</span></td></tr>
Line 22:		Line 23:
	</div>		</div>
	<div class="pdbe-citations 5gmn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gmn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase\|Carbonic anhydrase]]
	== References ==		== References ==
	<references/>		<references/>
Line 27:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
	[[Category: Hwang, K Y]]		[[Category: Hwang, K Y]]
	[[Category: Kim, H T]]		[[Category: Kim, H T]]

OCA at 13:39, 24 May 2017

OCA — Wed, 24 May 2017 13:39:06 GMT

←Older revision		Revision as of 13:39, 24 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gmn is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of human carbonic anhydrase II in complex with polmacoxib==
		+	<StructureSection load='5gmn' size='340' side='right' caption='[[5gmn]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gmn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GMN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GMN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=949:4-[3-(3-FLUOROPHENYL)-5,5-DIMETHYL-4-OXIDANYLIDENE-FURAN-2-YL]BENZENESULFONAMIDE'>949</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">[[5gmm\|5gmm]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Carbonate_dehydratase Carbonate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.1 4.2.1.1] </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=5gmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gmn OCA], [http://pdbe.org/5gmn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gmn RCSB], [http://www.ebi.ac.uk/pdbsum/5gmn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gmn ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Defects in CA2 are the cause of osteopetrosis autosomal recessive type 3 (OPTB3) [MIM:[http://omim.org/entry/259730 259730]]; also known as osteopetrosis with renal tubular acidosis, carbonic anhydrase II deficiency syndrome, Guibaud-Vainsel syndrome or marble brain disease. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. The disorder occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Autosomal recessive osteopetrosis is usually associated with normal or elevated amount of non-functional osteoclasts. OPTB3 is associated with renal tubular acidosis, cerebral calcification (marble brain disease) and in some cases with mental retardation.<ref>PMID:1928091</ref> <ref>PMID:1542674</ref> <ref>PMID:8834238</ref> <ref>PMID:9143915</ref> <ref>PMID:15300855</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAH2_HUMAN CAH2_HUMAN]] Essential for bone resorption and osteoclast differentiation (By similarity). Reversible hydration of carbon dioxide. Can hydrate cyanamide to urea. Involved in the regulation of fluid secretion into the anterior chamber of the eye.<ref>PMID:10550681</ref> <ref>PMID:11831900</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Polmacoxib is not only a selective COX-2 inhibitor but also a potent inhibitor of carbonic anhydrases (CAs). Both CA I and CA II are highly expressed in the GI tract and kidneys, organs that are also thought to be the sites at which selective COX-2 inhibitors show their side effects. By inhibition assays, we show that both CA I and CA II are strongly inhibited by polmacoxib, while CA II also demonstrates direct competition with COX-2. To understand, at the molecular level, how polmacoxib interacts with CA I and II, we solved the first crystal structures of CA I and CA II in complex with polmacoxib, at 2.0 A and 1.8 A, respectively. Interestingly, three polmacoxib molecules bind to the active site of CA I, whereas only one molecule binds CA II. In the active site, the three molecules of polmacoxib organize itself along hydrophobic interaction as "stack-on-formation", and fully occupy a cone-shaped active pocket in CA I. The binding mode of polmacoxib to CA II was found different than its binding to celecoxib and valdecoxib. Our results provide structural insight into inhibition of CA I and CA II by polmacoxib, to assess its potential clinical efficacy.

-	~~Authors:~~ Kim, H.T., ~~Hwang, K~~.Y.	+	Structural insight into the inhibition of carbonic anhydrase by the COX-2-selective inhibitor polmacoxib (CG100649).,Kim HT, Cha H, Hwang KY Biochem Biophys Res Commun. 2016 Sep 9;478(1):1-6. doi:, 10.1016/j.bbrc.2016.07.114. Epub 2016 Jul 27. PMID:27475498<ref>PMID:27475498</ref>

-	~~Description: Crystal structure~~ of ~~human carbonic anhydrase II in complex with polmacoxib~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Kim, H.T]]	+	<div class="pdbe-citations 5gmn" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Hwang, K.Y~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Hwang, K Y]]
		+	[[Category: Kim, H T]]
		+	[[Category: Complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Lyase]]

OCA at 08:59, 9 March 2017

OCA — Thu, 09 Mar 2017 08:59:38 GMT

←Older revision		Revision as of 08:59, 9 March 2017
Line 7:		Line 7:
	Description: Crystal structure of human carbonic anhydrase II in complex with polmacoxib		Description: Crystal structure of human carbonic anhydrase II in complex with polmacoxib
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Hwang, K.Y]]
	[[Category: Kim, H.T]]		[[Category: Kim, H.T]]
		+	[[Category: Hwang, K.Y]]

OCA at 08:24, 21 September 2016

OCA — Wed, 21 Sep 2016 08:24:03 GMT

←Older revision		Revision as of 08:24, 21 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gmn is ON HOLD	+	The entry 5gmn is ON HOLD until Paper Publication

	Authors: Kim, H.T., Hwang, K.Y.		Authors: Kim, H.T., Hwang, K.Y.

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

OCA — Tue, 26 Jul 2016 09:47:20 GMT

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

←Older revision

Revision as of 09:47, 26 July 2016

OCA: New page: '''Unreleased structure''' The entry 5gmn is ON HOLD Authors: Kim, H.T., Hwang, K.Y. Description: Crystal structure of human carbonic anhydrase II in complex with polmacoxib [[Category...

OCA — Tue, 26 Jul 2016 09:47:19 GMT

New page: '''Unreleased structure''' The entry 5gmn is ON HOLD Authors: Kim, H.T., Hwang, K.Y. Description: Crystal structure of human carbonic anhydrase II in complex with polmacoxib [[Category...

New page

'''Unreleased structure'''

The entry 5gmn is ON HOLD

Authors: Kim, H.T., Hwang, K.Y.

Description: Crystal structure of human carbonic anhydrase II in complex with polmacoxib
[[Category: Unreleased Structures]]
[[Category: Hwang, K.Y]]
[[Category: Kim, H.T]]