6z04 - Revision history

OCA at 13:39, 24 January 2024

2024-01-24T13:39:12Z

←Older revision		Revision as of 13:39, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6z04' size='340' side='right'caption='[[6z04]], [[Resolution\|resolution]] 1.05Å' scene=''>		<StructureSection load='6z04' size='340' side='right'caption='[[6z04]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6z04]] 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=6Z04 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Z04 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z04]] 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=6Z04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z04 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=Q3W:Carborane+nido~~-~~butyl-sulfonamide'>Q3W</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]] 1.05Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|Related:]]</b></td><td class="sblockDat">[[6yzj\|6yzj]], [[6yzl\|6yzl]], [[6yzn\|6yzn]], [[6yzv\|6yzv]], [[6yzt\|6yzt]], [[6yzk\|6yzk]], [[6yzm\|6yzm]], [[6yzo\|6yzo]], [[6yzp\|6yzp]], [[6yzq\|6yzq]], [[6yzr\|6yzr]], [[6yzs\|6yzs]], [[6yzu\|6yzu]], [[6yzw\|6yzw]], [[6yzx\|6yzx]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=Q3W:Carborane+nido-butyl-sulfonamide'>Q3W</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=6z04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z04 OCA], [https://pdbe.org/6z04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z04 RCSB], [https://www.ebi.ac.uk/pdbsum/6z04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z04 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~~://proteopedia.org/fgij/fg.htm?mol=6z04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z04 OCA], [~~http~~://pdbe.org/6z04 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6z04 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6z04 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6z04 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 23:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6z04" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6z04" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[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: Large Structures]]
-	[[Category: Brynda, J]]	+	[[Category: Brynda J]]
-	[[Category: Kugler, M]]	+	[[Category: Kugler M]]
-	[[Category: Pospisilova, K]]	+	[[Category: Pospisilova K]]
-	[[Category: Rezacova, P]]	+	[[Category: Rezacova P]]
-	~~[[Category: Ca inhibitor]]~~	+
-	~~[[Category: Carbonic anhydrase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 07:38, 4 November 2020

2020-11-04T07:38:35Z

←Older revision		Revision as of 07:38, 4 November 2020
Line 1:		Line 1:

	==Nido-carborane butyl-sulfonamide in complex with CA IX mimic==		==Nido-carborane butyl-sulfonamide in complex with CA IX mimic==
-	<StructureSection load='6z04' size='340' side='right'caption='[[6z04]]' scene=''>	+	<StructureSection load='6z04' size='340' side='right'caption='[[6z04]], [[Resolution\|resolution]] 1.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z04 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z04 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6z04]] 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=6Z04 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z04 FirstGlance]. <br>
-	</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=6z04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z04 OCA], [http://pdbe.org/6z04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z04 RCSB], [http://www.ebi.ac.uk/pdbsum/6z04 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z04 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=Q3W:Carborane+nido-butyl-sulfonamide'>Q3W</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">[[6yzj\|6yzj]], [[6yzl\|6yzl]], [[6yzn\|6yzn]], [[6yzv\|6yzv]], [[6yzt\|6yzt]], [[6yzk\|6yzk]], [[6yzm\|6yzm]], [[6yzo\|6yzo]], [[6yzp\|6yzp]], [[6yzq\|6yzq]], [[6yzr\|6yzr]], [[6yzs\|6yzs]], [[6yzu\|6yzu]], [[6yzw\|6yzw]], [[6yzx\|6yzx]]</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6z04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z04 OCA], [http://pdbe.org/6z04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z04 RCSB], [http://www.ebi.ac.uk/pdbsum/6z04 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z04 ProSAT]</span></td></tr>
	</table>		</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 ==
		+	Human carbonic anhydrase IX (CA IX), a protein specifically expressed on the surface of solid tumour cells, represents a validated target both for anticancer therapy and diagnostics. We recently identified sulfonamide dicarbaboranes as promising inhibitors of CA IX with favourable activities both in vitro and in vivo. To explain their selectivity and potency, we performed detailed X-ray structural analysis of their interactions within the active sites of CA IX and CA II. Series of compounds bearing various aliphatic linkers between the dicarbaborane cluster and sulfonamide group were examined. Preferential binding towards the hydrophobic part of the active site cavity was observed. Selectivity towards CA IX lies in the shape complementarity of the dicarbaborane cluster with a specific CA IX hydrophobic patch containing V131 residue. The bulky side chain of F131 residue in CA II alters the shape of the catalytic cavity, disrupting favourable interactions of the spherical dicarbaborane cluster.
		+
		+	The structural basis for the selectivity of sulfonamido dicarbaboranes toward cancer-associated carbonic anhydrase IX.,Kugler M, Holub J, Brynda J, Pospisilova K, Anwar SE, Bavol D, Havranek M, Kral V, Fabry M, Gruner B, Rezacova P J Enzyme Inhib Med Chem. 2020 Dec;35(1):1800-1810. doi:, 10.1080/14756366.2020.1816996. PMID:32962427<ref>PMID:32962427</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6z04" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brynda J]]	+	[[Category: Brynda, J]]
-	[[Category: Kugler M]]	+	[[Category: Kugler, M]]
-	[[Category: Pospisilova K]]	+	[[Category: Pospisilova, K]]
-	[[Category: Rezacova P]]	+	[[Category: Rezacova, P]]
		+	[[Category: Ca inhibitor]]
		+	[[Category: Carbonic anhydrase]]
		+	[[Category: Lyase]]

OCA at 20:35, 28 October 2020

2020-10-28T20:35:32Z

←Older revision		Revision as of 20:35, 28 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6z04 ~~is ON HOLD until Paper Publication~~	+	==Nido-carborane butyl-sulfonamide in complex with CA IX mimic==
-		+	<StructureSection load='6z04' size='340' side='right'caption='[[6z04]]' scene=''>
-	~~Authors~~: ~~Kugler~~, M., ~~Brynda, J~~., ~~Pospisilova, K~~., ~~Rezacova~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z04 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Z04 FirstGlance]. <br>
-	~~Description: Nido-carborane butyl-sulfonamide in complex with CA IX mimic~~	+	</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=6z04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z04 OCA], [http://pdbe.org/6z04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6z04 RCSB], [http://www.ebi.ac.uk/pdbsum/6z04 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6z04 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Pospisilova, K~~]]	+	__TOC__
-	[[Category: ~~Rezacova, P~~]]	+	</StructureSection>
-	[[Category: ~~Brynda, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kugler, M~~]]	+	[[Category: Brynda J]]
		+	[[Category: Kugler M]]
		+	[[Category: Pospisilova K]]
		+	[[Category: Rezacova P]]

OCA at 04:28, 20 May 2020

2020-05-20T04:28:48Z

←Older revision		Revision as of 04:28, 20 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6z04 is ON HOLD	+	The entry 6z04 is ON HOLD until Paper Publication

	Authors: Kugler, M., Brynda, J., Pospisilova, K., Rezacova, P.		Authors: Kugler, M., Brynda, J., Pospisilova, K., Rezacova, P.

-	Description: ~~Carborane~~ butyl-sulfonamide in complex with CA IX mimic	+	Description: Nido-carborane butyl-sulfonamide in complex with CA IX mimic
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pospisilova, K]]		[[Category: Pospisilova, K]]
-	[[Category: Brynda, J]]
	[[Category: Rezacova, P]]		[[Category: Rezacova, P]]
		+	[[Category: Brynda, J]]
	[[Category: Kugler, M]]		[[Category: Kugler, M]]

OCA: Protected "6z04" [edit=sysop:move=sysop]

2020-05-13T04:20:31Z

Protected "6z04" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:20, 13 May 2020

OCA: New page: '''Unreleased structure''' The entry 6z04 is ON HOLD Authors: Kugler, M., Brynda, J., Pospisilova, K., Rezacova, P. Description: Carborane butyl-sulfonamide in complex with CA IX mimic...

2020-05-13T04:20:30Z

New page: '''Unreleased structure''' The entry 6z04 is ON HOLD Authors: Kugler, M., Brynda, J., Pospisilova, K., Rezacova, P. Description: Carborane butyl-sulfonamide in complex with CA IX mimic...

New page

'''Unreleased structure'''

The entry 6z04 is ON HOLD

Authors: Kugler, M., Brynda, J., Pospisilova, K., Rezacova, P.

Description: Carborane butyl-sulfonamide in complex with CA IX mimic
[[Category: Unreleased Structures]]
[[Category: Pospisilova, K]]
[[Category: Brynda, J]]
[[Category: Rezacova, P]]
[[Category: Kugler, M]]