5tzc: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal Structure of human PDE2a in complex with (5S)-1-[(3-bromo-4-fluorophenyl)carbonyl]-3,3-difluoro-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}piperidine==
-<StructureSection load='5tzc' size='340' side='right' caption='[[5tzc]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
+<StructureSection load='5tzc' size='340' side='right'caption='[[5tzc]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5tzc]] is a 4 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=5TZC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TZC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5tzc]] is a 4 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=5TZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TZC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7OJ:(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE'>7OJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.36&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5tz3|5tz3]], [[5tza|5tza]], [[5tzh|5tzh]], [[5tzw|5tzw]], [[5tzx|5tzx]], [[5tzz|5tzz]], [[5u00|5u00]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7OJ:(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE'>7OJ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">PDE2A ([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=5tzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzc OCA], [https://pdbe.org/5tzc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tzc RCSB], [https://www.ebi.ac.uk/pdbsum/5tzc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzc 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/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </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=5tzc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tzc OCA], [http://pdbe.org/5tzc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tzc RCSB], [http://www.ebi.ac.uk/pdbsum/5tzc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tzc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PDE2A_HUMAN PDE2A_HUMAN]] Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes.<ref>PMID:15938621</ref> <ref>PMID:19828435</ref>
+[https://www.uniprot.org/uniprot/PDE2A_HUMAN PDE2A_HUMAN] Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes.<ref>PMID:15938621</ref> <ref>PMID:19828435</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-A series of potent and selective [1,2,4]triazolo[1,5-a]pyrimidine PDE2a inhibitors is reported. The design and improvement of the binding properties of this series was achieved using X-ray crystal structures in conjunction with careful analysis of electronic and structural requirements for the PDE2a enzyme. One of the lead compounds, compound 27 (DNS-8254), was identified as a potent and highly selective PDE2a enzyme inhibitor with favorable rat pharmacokinetic properties. Interestingly, the increased potency of compound 27 was facilitated by the formation of a halogen bond with the oxygen of Tyr827 present in the PDE2a active site. In vivo, compound 27 demonstrated significant memory enhancing effects in a rat model of novel object recognition. Taken together, these data suggest that compound 27 may be a useful tool to explore the pharmacology of selective PDE2a inhibition.
-Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.,Gomez L, Massari ME, Vickers T, Freestone G, Vernier W, Ly K, Xu R, McCarrick M, Marrone T, Metz M, Yan YG, Yoder ZW, Lemus R, Broadbent NJ, Barido R, Warren N, Schmelzer K, Neul D, Lee D, Andersen CB, Sebring K, Aertgeerts K, Zhou X, Tabatabaei A, Peters M, Breitenbucher JG J Med Chem. 2017 Feb 21. doi: 10.1021/acs.jmedchem.6b01793. PMID:28165743<ref>PMID:28165743</ref>
+==See Also==
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5tzc" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
+[[Category: Large Structures]]
-[[Category: Aertgeerts, K]]
+[[Category: Aertgeerts K]]
-[[Category: Xu, R]]
+[[Category: Xu R]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Phosphodiesterase]]