5llc - Revision history

OCA at 18:33, 18 October 2023

OCA — Wed, 18 Oct 2023 18:33:13 GMT

←Older revision		Revision as of 18:33, 18 October 2023
Line 1:		Line 1:

	==Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide==		==Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide==
-	<StructureSection load='5llc' size='340' side='right' caption='[[5llc]], [[Resolution\|resolution]] 1.10Å' scene=''>	+	<StructureSection load='5llc' size='340' side='right'caption='[[5llc]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5llc]] 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=5LLC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LLC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5llc]] 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=5LLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LLC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=V26:2,3,6-tris(fluoranyl)-5-(methylamino)-4-(2-phenylethylsulfonyl)benzenesulfonamide'>V26</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]] 1.1Å</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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=V26:2,3,6-tris(fluoranyl)-5-(methylamino)-4-(2-phenylethylsulfonyl)benzenesulfonamide'>V26</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=5llc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llc OCA], [https://pdbe.org/5llc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5llc RCSB], [https://www.ebi.ac.uk/pdbsum/5llc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5llc 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=5llc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llc OCA], [~~http~~://pdbe.org/5llc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5llc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5llc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5llc 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 24:		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: Grazulis, S]]	+	[[Category: Grazulis S]]
-	[[Category: Manakova, E]]	+	[[Category: Manakova E]]
-	[[Category: Smirnov, A]]	+	[[Category: Smirnov A]]
-	~~[[Category: Benzenesulfonamide]]~~	+
-	~~[[Category: Carbonic anhydrase]]~~	+
-	~~[[Category: Drug design]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Lyase-lyase inhibitor complex]]~~	+
-	~~[[Category: Metal-binding~~]]	+

OCA at 05:46, 16 May 2018

OCA — Wed, 16 May 2018 05:46:12 GMT

←Older revision		Revision as of 05:46, 16 May 2018
Line 13:		Line 13:
	== 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>		[[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 ==
		+	The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta-substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders-the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders-the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.
		+
		+	Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding.,Smirnov A, Zubriene A, Manakova E, Grazulis S, Matulis D PeerJ. 2018 Feb 26;6:e4412. doi: 10.7717/peerj.4412. eCollection 2018. PMID:29503769<ref>PMID:29503769</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5llc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Carbonic anhydrase\|Carbonic anhydrase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:50, 15 November 2017

OCA — Wed, 15 Nov 2017 23:50:56 GMT

←Older revision		Revision as of 23:50, 15 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5llc is ON HOLD until Paper Publication~~	+	==Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide==
-		+	<StructureSection load='5llc' size='340' side='right' caption='[[5llc]], [[Resolution\|resolution]] 1.10Å' scene=''>
-	~~Authors: Manakova, E., Smirnov, A., Grazulis, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5llc]] 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=5LLC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LLC FirstGlance]. <br>
-	~~Description:~~ Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=V26:2,3,6-tris(fluoranyl)-5-(methylamino)-4-(2-phenylethylsulfonyl)benzenesulfonamide'>V26</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5llc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5llc OCA], [http://pdbe.org/5llc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5llc RCSB], [http://www.ebi.ac.uk/pdbsum/5llc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5llc 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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
		+	[[Category: Human]]
		+	[[Category: Grazulis, S]]
	[[Category: Manakova, E]]		[[Category: Manakova, E]]
-	[[Category: Grazulis, S]]
	[[Category: Smirnov, A]]		[[Category: Smirnov, A]]
		+	[[Category: Benzenesulfonamide]]
		+	[[Category: Carbonic anhydrase]]
		+	[[Category: Drug design]]
		+	[[Category: Lyase]]
		+	[[Category: Lyase-lyase inhibitor complex]]
		+	[[Category: Metal-binding]]

OCA at 10:43, 9 March 2017

OCA — Thu, 09 Mar 2017 10:43:35 GMT

←Older revision		Revision as of 10:43, 9 March 2017
Line 7:		Line 7:
	Description: Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide		Description: Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Manakova, E]]
	[[Category: Grazulis, S]]		[[Category: Grazulis, S]]
	[[Category: Smirnov, A]]		[[Category: Smirnov, A]]
-	[[Category: Manakova, E]]

OCA at 14:59, 9 September 2016

OCA — Fri, 09 Sep 2016 14:59:57 GMT

←Older revision		Revision as of 14:59, 9 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Manakova, E., Smirnov, A., Grazulis, S.		Authors: Manakova, E., Smirnov, A., Grazulis, S.

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

OCA — Thu, 04 Aug 2016 02:57:13 GMT

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

←Older revision

Revision as of 02:57, 4 August 2016

OCA: New page: '''Unreleased structure''' The entry 5llc is ON HOLD Authors: Manakova, E., Smirnov, A., Grazulis, S. Description: Crystal structure of human carbonic anhydrase isozyme II with 3-(Meth...

OCA — Thu, 04 Aug 2016 02:57:12 GMT

New page: '''Unreleased structure''' The entry 5llc is ON HOLD Authors: Manakova, E., Smirnov, A., Grazulis, S. Description: Crystal structure of human carbonic anhydrase isozyme II with 3-(Meth...

New page

'''Unreleased structure'''

The entry 5llc is ON HOLD

Authors: Manakova, E., Smirnov, A., Grazulis, S.

Description: Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide
[[Category: Unreleased Structures]]
[[Category: Grazulis, S]]
[[Category: Smirnov, A]]
[[Category: Manakova, E]]