3hmv - Revision history

OCA at 08:27, 20 March 2024

OCA — Wed, 20 Mar 2024 08:27:14 GMT

←Older revision		Revision as of 08:27, 20 March 2024
Line 3:		Line 3:
	<StructureSection load='3hmv' size='340' side='right'caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='3hmv' size='340' side='right'caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmv]] is a 2 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=3HMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</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]] 2.23Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE4B, DPDE4 ([https://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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[https://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [https://pdbe.org/3hmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [https://www.ebi.ac.uk/pdbsum/3hmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmv ProSAT]</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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [https://pdbe.org/3hmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [https://www.ebi.ac.uk/pdbsum/3hmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>	+	[https://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hmv ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hmv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	A PDE4B over 4D-selective inhibitor programme was initiated to capitalise on the recently discovered predominance of the PDE4B subtype in inflammatory cell regulation. The SAR of a tetrahydrobenzothiophene (THBT) series did not agree with either of two proposed docking modes in the 4B binding site. A subsequent X-ray co-crystal structure determination revealed that the THBT ligand displaces the Gln-443 residue, invariably ligand-anchoring in previous PDE4 co-crystal structures, and even shifts helix-15 by 1-2A. For the first time, several residues of the C-terminus previously proposed to be involved in subtype selectivity are resolved and three of them extend into the ligand binding site potentially allowing for selective drug design.
-
-	Identification of PDE4B Over 4D subtype-selective inhibitors revealing an unprecedented binding mode.,Kranz M, Wall M, Evans B, Miah A, Ballantine S, Delves C, Dombroski B, Gross J, Schneck J, Villa JP, Neu M, Somers DO Bioorg Med Chem. 2009 Jul 15;17(14):5336-41. Epub 2009 Apr 5. PMID:19525117<ref>PMID:19525117</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3hmv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3',5'-cyclic-nucleotide phosphodiesterase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Neu, M]]	+	[[Category: Neu M]]
-	[[Category: Somers~~, D O]]~~	+	[[Category: Somers DO]]
-	~~[[Category: Alternative splicing]]~~	+
-	~~[[Category: Camp]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pde]]~~	+
-	~~[[Category: Phosphodiesterase]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Polymorphism~~]]	+

OCA at 12:52, 23 March 2022

OCA — Wed, 23 Mar 2022 12:52:57 GMT

←Older revision		Revision as of 12:52, 23 March 2022
Line 1:		Line 1:

	==Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor==		==Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor==
-	<StructureSection load='3hmv' size='340' side='right' caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>	+	<StructureSection load='3hmv' size='340' side='right'caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmv]] is a 2 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=3HMV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</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">PDE4B, DPDE4 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE4B, DPDE4 ([https://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/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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [https://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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [~~http~~://pdbe.org/3hmv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hmv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmv ProSAT]</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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [https://pdbe.org/3hmv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [https://www.ebi.ac.uk/pdbsum/3hmv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>	+	[[https://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Phosphodiesterase\|Phosphodiesterase]]	+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Neu, M]]		[[Category: Neu, M]]
	[[Category: Somers, D O]]		[[Category: Somers, D O]]

OCA at 08:24, 12 December 2018

OCA — Wed, 12 Dec 2018 08:24:14 GMT

←Older revision		Revision as of 08:24, 12 December 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hmv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hmv_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	[[Category: Neu, M]]		[[Category: Neu, M]]
	[[Category: Somers, D O]]		[[Category: Somers, D O]]
		+	[[Category: Alternative splicing]]
	[[Category: Camp]]		[[Category: Camp]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
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	[[Category: Phosphodiesterase]]		[[Category: Phosphodiesterase]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
		+	[[Category: Polymorphism]]

OCA at 23:29, 5 August 2016

OCA — Fri, 05 Aug 2016 23:29:06 GMT

←Older revision		Revision as of 23:29, 5 August 2016
Line 1:		Line 1:
		+
	==Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor==		==Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor==
	<StructureSection load='3hmv' size='340' side='right' caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>		<StructureSection load='3hmv' size='340' side='right' caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmv]] is a 2 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=3HMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</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">PDE4B, DPDE4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE4B, DPDE4 ([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/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='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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [http://www.ebi.ac.uk/pdbsum/3hmv PDBsum]</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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [http://pdbe.org/3hmv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [http://www.ebi.ac.uk/pdbsum/3hmv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmv ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hmv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3hmv" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Neu, M]]		[[Category: Neu, M]]
	[[Category: Somers, D O]]		[[Category: Somers, D O]]

OCA at 06:47, 25 December 2014

OCA — Thu, 25 Dec 2014 06:47:33 GMT

←Older revision		Revision as of 06:47, 25 December 2014
Line 8:		Line 8:
	<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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [http://www.ebi.ac.uk/pdbsum/3hmv PDBsum]</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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [http://www.ebi.ac.uk/pdbsum/3hmv PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDE4B_HUMAN PDE4B_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes. May be involved in mediating central nervous system effects of therapeutic agents ranging from antidepressants to antiasthmatic and anti-inflammatory agents.<ref>PMID:10846163</ref> <ref>PMID:15003452</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:40, 8 December 2014

OCA — Mon, 08 Dec 2014 09:40:15 GMT

←Older revision		Revision as of 09:40, 8 December 2014
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-	[[~~Image:~~3hmv.~~png~~\|~~left~~\|200px]]	+	==Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor==
		+	<StructureSection load='3hmv' size='340' side='right' caption='[[3hmv]], [[Resolution\|resolution]] 2.23Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMV FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HBT:(6S)-6-METHYL-2-{[(2-NITROPHENYL)CARBONYL]AMINO}-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-3-CARBOXAMIDE'>HBT</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">PDE4B, DPDE4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3hmv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmv RCSB], [http://www.ebi.ac.uk/pdbsum/3hmv PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hmv_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A PDE4B over 4D-selective inhibitor programme was initiated to capitalise on the recently discovered predominance of the PDE4B subtype in inflammatory cell regulation. The SAR of a tetrahydrobenzothiophene (THBT) series did not agree with either of two proposed docking modes in the 4B binding site. A subsequent X-ray co-crystal structure determination revealed that the THBT ligand displaces the Gln-443 residue, invariably ligand-anchoring in previous PDE4 co-crystal structures, and even shifts helix-15 by 1-2A. For the first time, several residues of the C-terminus previously proposed to be involved in subtype selectivity are resolved and three of them extend into the ligand binding site potentially allowing for selective drug design.

-	~~{{STRUCTURE_3hmv\| PDB=3hmv \| SCENE= }}~~	+	Identification of PDE4B Over 4D subtype-selective inhibitors revealing an unprecedented binding mode.,Kranz M, Wall M, Evans B, Miah A, Ballantine S, Delves C, Dombroski B, Gross J, Schneck J, Villa JP, Neu M, Somers DO Bioorg Med Chem. 2009 Jul 15;17(14):5336-41. Epub 2009 Apr 5. PMID:19525117<ref>PMID:19525117</ref>

-	~~===Catalytic domain~~ of ~~human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19525117}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3hmv]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].~~	+

	==See Also==		==See Also==
	*[[Phosphodiesterase\|Phosphodiesterase]]		*[[Phosphodiesterase\|Phosphodiesterase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019525117<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Neu, M.]]	+	[[Category: Neu, M]]
-	[[Category: Somers, D O.]]	+	[[Category: Somers, D O]]
	[[Category: Camp]]		[[Category: Camp]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 13:49, 20 October 2012

OCA — Sat, 20 Oct 2012 13:49:30 GMT

←Older revision		Revision as of 13:49, 20 October 2012
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	==About this Structure==		==About this Structure==
-	[[3hmv]] is a 2 chain structure ~~of [[Phosphodiesterase]]~~ with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].	+	[[3hmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].

	==See Also==		==See Also==

OCA at 13:13, 26 July 2012

OCA — Thu, 26 Jul 2012 13:13:54 GMT

←Older revision		Revision as of 13:13, 26 July 2012
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	[[Image:3hmv.png\|left\|200px]]		[[Image:3hmv.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3hmv\| PDB=3hmv \| SCENE= }}		{{STRUCTURE_3hmv\| PDB=3hmv \| SCENE= }}

	===Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor===		===Catalytic domain of human phosphodiesterase 4B2B in complex with a tetrahydrobenzothiophene inhibitor===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19525117}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19525117 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19525117}}		{{ABSTRACT_PUBMED_19525117}}

	==About this Structure==		==About this Structure==
-	[[3hmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].	+	[[3hmv]] is a 2 chain structure of [[Phosphodiesterase]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].
		+
		+	==See Also==
		+	*[[Phosphodiesterase\|Phosphodiesterase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19525117~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019525117</ref><references group="xtra"/>
	[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]		[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Neu, M.]]		[[Category: Neu, M.]]
	[[Category: Somers, D O.]]		[[Category: Somers, D O.]]
-	[[Category: Alternative splicing]]
	[[Category: Camp]]		[[Category: Camp]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
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	[[Category: Phosphodiesterase]]		[[Category: Phosphodiesterase]]
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
-	[[Category: Polymorphism]]

OCA: Protected "3hmv" [edit=sysop:move=sysop]

OCA — Wed, 29 Dec 2010 18:30:53 GMT

Protected "3hmv" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:30, 29 December 2010

OCA at 18:30, 29 December 2010

OCA — Wed, 29 Dec 2010 18:30:51 GMT

←Older revision		Revision as of 18:30, 29 December 2010
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-	{{Seed}}
	[[Image:3hmv.png\|left\|200px]]		[[Image:3hmv.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3HMV~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].	+	[[3hmv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HMV OCA].

	==Reference==		==Reference==
Line 35:		Line 34:
	[[Category: Phosphoprotein]]		[[Category: Phosphoprotein]]
	[[Category: Polymorphism]]		[[Category: Polymorphism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:34:48 2010''