6kjz - Revision history

OCA at 10:35, 22 November 2023

OCA — Wed, 22 Nov 2023 10:35:09 GMT

←Older revision		Revision as of 10:35, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kjz]] 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=6KJZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kjz]] 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=6KJZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KJZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MKU:5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2-EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE'>MKU</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]] 2.200001Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PDE4D, DPDE3 ([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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MKU:5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2-EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE'>MKU</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/3',5'-cyclic-AMP_phosphodiesterase 3',5'-cyclic-AMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.53 3.1.4.53] </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=6kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kjz OCA], [https://pdbe.org/6kjz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kjz RCSB], [https://www.ebi.ac.uk/pdbsum/6kjz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kjz ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kjz OCA], [~~http~~://pdbe.org/6kjz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kjz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kjz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kjz ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN]] Note=Genetic variations in PDE4D might be associated with susceptibility to stroke. PubMed:17006457 states that association with stroke has to be considered with caution. Defects in PDE4D are the cause of acrodysostosis type 2, with or without hormone resistance (ACRDYS2) [MIM:[~~http~~://omim.org/entry/614613 614613]]. ACRDYS2 is a pleiotropic disorder characterized by skeletal, endocrine, and neurological abnormalities. Skeletal features include brachycephaly, midface hypoplasia with a small upturned nose, brachydactyly, and lumbar spinal stenosis. Endocrine abnormalities include hypothyroidism and hypogonadism in males and irregular menses in females. Developmental disability is a common finding but is variable in severity and can be associated with significant behavioral problems.<ref>PMID:22464250</ref>	+	[https://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN] Note=Genetic variations in PDE4D might be associated with susceptibility to stroke. PubMed:17006457 states that association with stroke has to be considered with caution. Defects in PDE4D are the cause of acrodysostosis type 2, with or without hormone resistance (ACRDYS2) [MIM:[https://omim.org/entry/614613 614613]. ACRDYS2 is a pleiotropic disorder characterized by skeletal, endocrine, and neurological abnormalities. Skeletal features include brachycephaly, midface hypoplasia with a small upturned nose, brachydactyly, and lumbar spinal stenosis. Endocrine abnormalities include hypothyroidism and hypogonadism in males and irregular menses in females. Developmental disability is a common finding but is variable in severity and can be associated with significant behavioral problems.<ref>PMID:22464250</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes.<ref>PMID:15260978</ref> <ref>PMID:15576036</ref>	+	[https://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes.<ref>PMID:15260978</ref> <ref>PMID:15576036</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6kjz" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kjz" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Phosphodiesterase 3D structures\|Phosphodiesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3',5'-cyclic-AMP phosphodiesterase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: He, X]]	+	[[Category: He X]]
-	[[Category: Huang, Y Y]]	+	[[Category: Huang Y-Y]]
-	[[Category: Luo, H B]]	+	[[Category: Luo H-B]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pde4 inhibitor~~]]	+

OCA at 05:44, 13 May 2020

OCA — Wed, 13 May 2020 05:44:59 GMT

←Older revision		Revision as of 05:44, 13 May 2020
Line 1:		Line 1:

-	==Crystal ~~strucure~~ of PDE4D catalytic domain complexed with compound 1==	+	==Crystal structure of PDE4D catalytic domain complexed with compound 1==
	<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 07:16, 8 April 2020

OCA — Wed, 08 Apr 2020 07:16:28 GMT

←Older revision		Revision as of 07:16, 8 April 2020
Line 3:		Line 3:
	<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KJZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KJZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kjz]] 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=6KJZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KJZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MKU:5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2-EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE'>MKU</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MKU:5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2-EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE'>MKU</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">PDE4D, DPDE3 ([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-AMP_phosphodiesterase 3',5'-cyclic-AMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.53 3.1.4.53] </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-AMP_phosphodiesterase 3',5'-cyclic-AMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.53 3.1.4.53] </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=6kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kjz OCA], [http://pdbe.org/6kjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kjz RCSB], [http://www.ebi.ac.uk/pdbsum/6kjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kjz ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kjz OCA], [http://pdbe.org/6kjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kjz RCSB], [http://www.ebi.ac.uk/pdbsum/6kjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kjz ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: 3',5'-cyclic-AMP phosphodiesterase]]		[[Category: 3',5'-cyclic-AMP phosphodiesterase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: He, X]]		[[Category: He, X]]

OCA at 09:39, 18 March 2020

OCA — Wed, 18 Mar 2020 09:39:50 GMT

←Older revision		Revision as of 09:39, 18 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kjz is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal strucure of PDE4D catalytic domain complexed with compound 1==
		+	<StructureSection load='6kjz' size='340' side='right'caption='[[6kjz]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kjz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KJZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KJZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MKU:5,9-DIHYDROXY-8-METHOXY-2,2-DIMETHYL-7-(3-METHYLBUT-2-EN-1-YL)-3,4-DIHYDRO-2H,6H-PYRANO[3,2-B]XANTHEN-6-ONE'>MKU</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/3',5'-cyclic-AMP_phosphodiesterase 3',5'-cyclic-AMP phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.53 3.1.4.53] </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=6kjz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kjz OCA], [http://pdbe.org/6kjz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kjz RCSB], [http://www.ebi.ac.uk/pdbsum/6kjz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kjz ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN]] Note=Genetic variations in PDE4D might be associated with susceptibility to stroke. PubMed:17006457 states that association with stroke has to be considered with caution. Defects in PDE4D are the cause of acrodysostosis type 2, with or without hormone resistance (ACRDYS2) [MIM:[http://omim.org/entry/614613 614613]]. ACRDYS2 is a pleiotropic disorder characterized by skeletal, endocrine, and neurological abnormalities. Skeletal features include brachycephaly, midface hypoplasia with a small upturned nose, brachydactyly, and lumbar spinal stenosis. Endocrine abnormalities include hypothyroidism and hypogonadism in males and irregular menses in females. Developmental disability is a common finding but is variable in severity and can be associated with significant behavioral problems.<ref>PMID:22464250</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PDE4D_HUMAN PDE4D_HUMAN]] Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes.<ref>PMID:15260978</ref> <ref>PMID:15576036</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	To validate PDE4 inhibitors as novel therapeutic agents against vascular dementia (VaD), 25 derivatives were discovered from the natural inhibitor alpha-mangostin (IC50 = 1.31 muM). Hit-to-lead optimization identified a novel and selective PDE4 inhibitor 4e (IC50 = 17 nM), which adopted a different binding pattern from PDE4 inhibitors roflumilast and rolipram. Oral administration of 4e at a dose of 10 mg/kg exhibited remarkable therapeutic effects in a VaD model and did not cause emesis to beagle dogs, indicating its potential as a novel anti-VaD agent.

-	~~Authors:~~ Huang, Y~~.-Y.~~, He, X., ~~Luo~~, H.-B.	+	Discovery and Optimization of alpha-Mangostin Derivatives as Novel PDE4 Inhibitors for the Treatment of Vascular Dementia.,Liang J, Huang YY, Zhou Q, Gao Y, Li Z, Wu D, Yu S, Guo L, Chen Z, Huang L, Liang SH, He X, Wu R, Luo HB J Med Chem. 2020 Mar 12. doi: 10.1021/acs.jmedchem.0c00060. PMID:32115956<ref>PMID:32115956</ref>

-	~~Description: Crystal strucure~~ of ~~PDE4D catalytic domain complexed with compound 1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Luo, H.-B~~]]	+	<div class="pdbe-citations 6kjz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 3',5'-cyclic-AMP phosphodiesterase]]
		+	[[Category: Large Structures]]
	[[Category: He, X]]		[[Category: He, X]]
-	[[Category: Huang, Y.-Y]]	+	[[Category: Huang, Y Y]]
		+	[[Category: Luo, H B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pde4 inhibitor]]

OCA at 04:06, 7 August 2019

OCA — Wed, 07 Aug 2019 04:06:45 GMT

←Older revision		Revision as of 04:06, 7 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kjz is ON HOLD	+	The entry 6kjz is ON HOLD until Paper Publication

	Authors: Huang, Y.-Y., He, X., Luo, H.-B.		Authors: Huang, Y.-Y., He, X., Luo, H.-B.

OCA: Protected "6kjz" [edit=sysop:move=sysop]

OCA — Wed, 31 Jul 2019 04:38:16 GMT

Protected "6kjz" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:38, 31 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kjz is ON HOLD Authors: Huang, Y.-Y., He, X., Luo, H.-B. Description: Crystal strucure of PDE4D catalytic domain complexed with compound 1 [[Categ...

OCA — Wed, 31 Jul 2019 04:38:14 GMT

New page: '''Unreleased structure''' The entry 6kjz is ON HOLD Authors: Huang, Y.-Y., He, X., Luo, H.-B. Description: Crystal strucure of PDE4D catalytic domain complexed with compound 1 [[Categ...

New page

'''Unreleased structure'''

The entry 6kjz is ON HOLD

Authors: Huang, Y.-Y., He, X., Luo, H.-B.

Description: Crystal strucure of PDE4D catalytic domain complexed with compound 1
[[Category: Unreleased Structures]]
[[Category: Luo, H.-B]]
[[Category: He, X]]
[[Category: Huang, Y.-Y]]