5lmd - Revision history

OCA at 18:34, 18 October 2023

2023-10-18T18:34:42Z

←Older revision		Revision as of 18:34, 18 October 2023
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	<StructureSection load='5lmd' size='340' side='right'caption='[[5lmd]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5lmd' size='340' side='right'caption='[[5lmd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmd]] 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=5LMD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmd]] 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=5LMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LMD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RC4:1-[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-4-YL]-3-(2-METHOXY-5-METHYL-PHENYL)UREA'>RC4</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]] 1.7Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RC4:1-[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-4-YL]-3-(2-METHOXY-5-METHYL-PHENYL)UREA'>RC4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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'>[https://proteopedia.org/fgij/fg.htm?mol=5lmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmd OCA], [https://pdbe.org/5lmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lmd RCSB], [https://www.ebi.ac.uk/pdbsum/5lmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmd ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5lmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmd OCA], [~~http~~://pdbe.org/5lmd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lmd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lmd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmd 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Carbonate dehydratase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Alterio, V]]	+	[[Category: Alterio V]]
-	[[Category: ~~Esposito, D~~]]	+	[[Category: De Simone G]]
-	[[Category: Fiore, A Di]]	+	[[Category: Di Fiore A]]
-	[[Category: ~~Simone, G De]]~~	+	[[Category: Esposito D]]
-	~~[[Category: Benzoxaborole]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Zinc enzyme~~]]	+

OCA at 10:42, 12 August 2020

2020-08-12T10:42:32Z

←Older revision		Revision as of 10:42, 12 August 2020
Line 1:		Line 1:

	==The crystal structure of hCA II in complex with a benzoxaborole inhibitor==		==The crystal structure of hCA II in complex with a benzoxaborole inhibitor==
-	<StructureSection load='5lmd' size='340' side='right' caption='[[5lmd]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5lmd' size='340' side='right'caption='[[5lmd]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LMD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmd]] 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=5LMD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LMD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RC4:1-[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-4-YL]-3-(2-METHOXY-5-METHYL-PHENYL)UREA'>RC4</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=RC4:1-[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-4-YL]-3-(2-METHOXY-5-METHYL-PHENYL)UREA'>RC4</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='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=5lmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmd OCA], [http://pdbe.org/5lmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmd RCSB], [http://www.ebi.ac.uk/pdbsum/5lmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmd ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5lmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmd OCA], [http://pdbe.org/5lmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmd RCSB], [http://www.ebi.ac.uk/pdbsum/5lmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmd ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5lmd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5lmd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase 3D structures\|Carbonic anhydrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Carbonate dehydratase]]		[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Alterio, V]]		[[Category: Alterio, V]]
	[[Category: Esposito, D]]		[[Category: Esposito, D]]

OCA at 17:22, 19 October 2016

2016-10-19T17:22:01Z

←Older revision		Revision as of 17:22, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5lmd is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The crystal structure of hCA II in complex with a benzoxaborole inhibitor==
		+	<StructureSection load='5lmd' size='340' side='right' caption='[[5lmd]], [[Resolution\|resolution]] 1.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lmd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RC4:1-[7,7-BIS(OXIDANYL)-8-OXA-7-BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-4-YL]-3-(2-METHOXY-5-METHYL-PHENYL)UREA'>RC4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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=5lmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmd OCA], [http://pdbe.org/5lmd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmd RCSB], [http://www.ebi.ac.uk/pdbsum/5lmd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmd 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 ==
		+	In this paper we report the synthesis of a series of benzoxaborole derivatives, their inhibition properties against some carbonic anhydrases (CAs), recognized as important drug targets, and the characterization of the binding mode of these molecules to the CA active site. Our data provide the first experimental evidence that benzoxaboroles can be efficiently used as CA inhibitors.

-	~~Authors: De Simone, G~~., Alterio, V., Esposito, D., Di Fiore, A.	+	Benzoxaborole as a new chemotype for carbonic anhydrase inhibition.,Alterio V, Cadoni R, Esposito D, Vullo D, Fiore AD, Monti SM, Caporale A, Ruvo M, Sechi M, Dumy P, Supuran CT, Simone G, Winum JY Chem Commun (Camb). 2016 Sep 29;52(80):11983-11986. PMID:27722534<ref>PMID:27722534</ref>

-	~~Description: The crystal structure~~ of ~~hCA II in complex with a benzoxaborole inhibitor~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Di Fiore, A]]~~	+	<div class="pdbe-citations 5lmd" style="background-color:#fffaf0;"></div>
-	~~[[Category: Esposito, D]]~~	+	== References ==
-	[[Category: ~~De Simone, G~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
	[[Category: Alterio, V]]		[[Category: Alterio, V]]
		+	[[Category: Esposito, D]]
		+	[[Category: Fiore, A Di]]
		+	[[Category: Simone, G De]]
		+	[[Category: Benzoxaborole]]
		+	[[Category: Inhibitor]]
		+	[[Category: Lyase]]
		+	[[Category: Zinc enzyme]]

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

2016-08-10T14:38:42Z

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

←Older revision

Revision as of 14:38, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5lmd is ON HOLD until Paper Publication Authors: De Simone, G., Alterio, V., Esposito, D., Di Fiore, A. Description: The crystal structure of hCA I...

2016-08-10T14:38:41Z

New page: '''Unreleased structure''' The entry 5lmd is ON HOLD until Paper Publication Authors: De Simone, G., Alterio, V., Esposito, D., Di Fiore, A. Description: The crystal structure of hCA I...

New page

'''Unreleased structure'''

The entry 5lmd is ON HOLD until Paper Publication

Authors: De Simone, G., Alterio, V., Esposito, D., Di Fiore, A.

Description: The crystal structure of hCA II in complex with a benzoxaborole inhibitor
[[Category: Unreleased Structures]]
[[Category: Di Fiore, A]]
[[Category: Esposito, D]]
[[Category: De Simone, G]]
[[Category: Alterio, V]]