5ny1 - Revision history

OCA at 12:15, 22 November 2023

OCA — Wed, 22 Nov 2023 12:15:47 GMT

←Older revision		Revision as of 12:15, 22 November 2023
Line 1:		Line 1:

	==Carbonic Anhydrase II Inhibitor RA10==		==Carbonic Anhydrase II Inhibitor RA10==
-	<StructureSection load='5ny1' size='340' side='right' caption='[[5ny1]], [[Resolution\|resolution]] 1.10Å' scene=''>	+	<StructureSection load='5ny1' size='340' side='right'caption='[[5ny1]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ny1]] 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=5NY1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ny1]] 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=5NY1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NY1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=9E5:3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide'>9E5</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~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nxg\|5nxg]]~~, [[~~5nxi~~\|~~5nxi]], [[5nxm\|5nxm]], [[5nxo\|5nxo]], [[5nxp\|5nxp]], [[5nxv\|5nxv]], [[5nxw\|5nxw~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9E5:3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide'>9E5</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=5ny1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny1 OCA], [https://pdbe.org/5ny1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ny1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ny1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny1 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=5ny1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny1 OCA], [~~http~~://pdbe.org/5ny1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ny1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ny1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny1 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: Brynda, J]]	+	[[Category: Brynda J]]
-	[[Category: Fanfrlik, J]]	+	[[Category: Fanfrlik J]]
-	[[Category: Horejsi, M]]	+	[[Category: Horejsi M]]
-	[[Category: Rezacova, P]]	+	[[Category: Rezacova P]]
-	~~[[Category: Ca inhibitor]]~~	+
-	~~[[Category: Carbonic anhydrase ii]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 06:28, 18 April 2018

OCA — Wed, 18 Apr 2018 06:28:03 GMT

←Older revision		Revision as of 06:28, 18 April 2018
Line 3:		Line 3:
	<StructureSection load='5ny1' size='340' side='right' caption='[[5ny1]], [[Resolution\|resolution]] 1.10Å' scene=''>		<StructureSection load='5ny1' size='340' side='right' caption='[[5ny1]], [[Resolution\|resolution]] 1.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ny1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NY1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ny1]] 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=5NY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NY1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9E5:3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide'>9E5</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=9E5:3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide'>9E5</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">[[5nxg\|5nxg]], [[5nxi\|5nxi]], [[5nxm\|5nxm]], [[5nxo\|5nxo]], [[5nxp\|5nxp]], [[5nxv\|5nxv]], [[5nxw\|5nxw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5nxg\|5nxg]], [[5nxi\|5nxi]], [[5nxm\|5nxm]], [[5nxo\|5nxo]], [[5nxp\|5nxp]], [[5nxv\|5nxv]], [[5nxw\|5nxw]]</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=5ny1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny1 OCA], [http://pdbe.org/5ny1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ny1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ny1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny1 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=5ny1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny1 OCA], [http://pdbe.org/5ny1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ny1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ny1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny1 ProSAT]</span></td></tr>
Line 22:		Line 23:
	</div>		</div>
	<div class="pdbe-citations 5ny1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ny1" 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: Brynda, J]]		[[Category: Brynda, J]]
	[[Category: Fanfrlik, J]]		[[Category: Fanfrlik, J]]

OCA at 06:50, 17 January 2018

OCA — Wed, 17 Jan 2018 06:50:10 GMT

←Older revision		Revision as of 06:50, 17 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ny1 is ~~ON HOLD~~	+	==Carbonic Anhydrase II Inhibitor RA10==
		+	<StructureSection load='5ny1' size='340' side='right' caption='[[5ny1]], [[Resolution\|resolution]] 1.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ny1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NY1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NY1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9E5:3,6,7-trimethyl-~{N}-[(4-sulfamoylphenyl)methyl]-1-benzofuran-2-carboxamide'>9E5</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">[[5nxg\|5nxg]], [[5nxi\|5nxi]], [[5nxm\|5nxm]], [[5nxo\|5nxo]], [[5nxp\|5nxp]], [[5nxv\|5nxv]], [[5nxw\|5nxw]]</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=5ny1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ny1 OCA], [http://pdbe.org/5ny1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ny1 RCSB], [http://www.ebi.ac.uk/pdbsum/5ny1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ny1 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 ==
		+	Accurate prediction of protein-ligand binding affinities is essential for hit-to-lead optimization and virtual screening. The reliability of scoring functions can be improved by implementing of quantum effects. Here, we demonstrate the ranking power of the semiempirical quantum mechanics (SQM)/implicit solvent (COSMO) scoring function using a challenging set of 10 inhibitors binding to carbonic anhydrase II via Zn2+ in the active site. This new dataset consists of the high-resolution (1.1 - 1.4 A) crystal structures and experimentally determined Ki values. It allowed us to evaluate the common approximations, such as representing the solvent implicitly or using a single target conformation combined with a set of ligand docking poses. The SQM/COSMO attained good correlation of R2 0.56 - 0.77 with the experimental inhibitory activities, benefiting from the careful handling of both noncovalent interactions (e.g. charge transfer) and solvation. This proof-of-concept study of SQM/COSMO ranking for metalloprotein-ligand systems demonstrates its potential for hit-to-lead applications.

-	~~Authors:~~ Brynda, J., Rezacova, P., ~~Horejsi~~, M., Fanfrlik, J.	+	Ranking Power of the SQM/COSMO Scoring Function on Carbonic Anhydrase II-Inhibitor Complexes.,Pecina A, Brynda J, Vrzal L, Gnanasekaran R, Horejsi M, Eyrilmez S, Rezac J, Lepsik M, Rezacova P, Hobza P, Majer P, Veverka V, Fanfrlik J Chemphyschem. 2018 Jan 8. doi: 10.1002/cphc.201701104. PMID:29316128<ref>PMID:29316128</ref>

-	~~Description~~: ~~Carbonic Anhydrase II Inhibitor RA10~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ny1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carbonate dehydratase]]
	[[Category: Brynda, J]]		[[Category: Brynda, J]]
-	[[Category: Rezacova, P]]
	[[Category: Fanfrlik, J]]		[[Category: Fanfrlik, J]]
	[[Category: Horejsi, M]]		[[Category: Horejsi, M]]
		+	[[Category: Rezacova, P]]
		+	[[Category: Ca inhibitor]]
		+	[[Category: Carbonic anhydrase ii]]
		+	[[Category: Lyase]]

OCA: Protected "5ny1" [edit=sysop:move=sysop]

OCA — Wed, 17 May 2017 12:25:07 GMT

Protected "5ny1" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:25, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5ny1 is ON HOLD Authors: Brynda, J., Rezacova, P., Horejsi, M., Fanfrlik, J. Description: Carbonic Anhydrase II Inhibitor RA10 [[Category: Unreleas...

OCA — Wed, 17 May 2017 12:25:06 GMT

New page: '''Unreleased structure''' The entry 5ny1 is ON HOLD Authors: Brynda, J., Rezacova, P., Horejsi, M., Fanfrlik, J. Description: Carbonic Anhydrase II Inhibitor RA10 [[Category: Unreleas...

New page

'''Unreleased structure'''

The entry 5ny1 is ON HOLD

Authors: Brynda, J., Rezacova, P., Horejsi, M., Fanfrlik, J.

Description: Carbonic Anhydrase II Inhibitor RA10
[[Category: Unreleased Structures]]
[[Category: Brynda, J]]
[[Category: Rezacova, P]]
[[Category: Fanfrlik, J]]
[[Category: Horejsi, M]]