5nxm
From Proteopedia
(Difference between revisions)
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==Carbonic Anhydrase II Inhibitor RA1== | ==Carbonic Anhydrase II Inhibitor RA1== | ||
- | <StructureSection load='5nxm' size='340' side='right' caption='[[5nxm]], [[Resolution|resolution]] 1.25Å' scene=''> | + | <StructureSection load='5nxm' size='340' side='right'caption='[[5nxm]], [[Resolution|resolution]] 1.25Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
- | <table><tr><td colspan='2'>[[5nxm]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NXM FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nxm]] 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=5NXM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NXM FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RA5:8-methoxy-2-oxidanylidene-~{N}-(4-sulfamoylphenyl)chromene-3-carboxamide'>RA5</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=RA5:8-methoxy-2-oxidanylidene-~{N}-(4-sulfamoylphenyl)chromene-3-carboxamide'>RA5</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]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5nxg|5nxg]], [[5nxi|5nxi]]</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=5nxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nxm OCA], [http://pdbe.org/5nxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nxm RCSB], [http://www.ebi.ac.uk/pdbsum/5nxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nxm 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=5nxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nxm OCA], [http://pdbe.org/5nxm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nxm RCSB], [http://www.ebi.ac.uk/pdbsum/5nxm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nxm ProSAT]</span></td></tr> | ||
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== 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 == | ||
+ | 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. | ||
+ | |||
+ | 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> | ||
+ | |||
+ | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
+ | </div> | ||
+ | <div class="pdbe-citations 5nxm" style="background-color:#fffaf0;"></div> | ||
+ | |||
+ | ==See Also== | ||
+ | *[[Carbonic anhydrase 3D structures|Carbonic anhydrase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Carbonate dehydratase]] | [[Category: Carbonate dehydratase]] | ||
+ | [[Category: Human]] | ||
+ | [[Category: Large Structures]] | ||
[[Category: Brynda, J]] | [[Category: Brynda, J]] | ||
[[Category: Fanfrlik, J]] | [[Category: Fanfrlik, J]] |
Revision as of 06:05, 12 June 2019
Carbonic Anhydrase II Inhibitor RA1
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