6g8f - Revision history

OCA at 07:17, 31 October 2018

OCA — Wed, 31 Oct 2018 07:17:46 GMT

←Older revision		Revision as of 07:17, 31 October 2018
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	<StructureSection load='6g8f' size='340' side='right' caption='[[6g8f]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='6g8f' size='340' side='right' caption='[[6g8f]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6g8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6g8f]] 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=6G8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G8F FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K0I:3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC+ACID'>K0I</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K0I:3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC+ACID'>K0I</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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">KDM6A, UTX ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6g8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g8f OCA], [http://pdbe.org/6g8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g8f RCSB], [http://www.ebi.ac.uk/pdbsum/6g8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g8f 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=6g8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g8f OCA], [http://pdbe.org/6g8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g8f RCSB], [http://www.ebi.ac.uk/pdbsum/6g8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g8f ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
	[[Category: Esposito, C]]		[[Category: Esposito, C]]

OCA at 08:13, 10 October 2018

OCA — Wed, 10 Oct 2018 08:13:02 GMT

←Older revision		Revision as of 08:13, 10 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~6g8f~~ is ~~ON HOLD~~	+	==Crystal structure of UTX complexed with GSK-J1==
		+	<StructureSection load='6g8f' size='340' side='right' caption='[[6g8f]], [[Resolution\|resolution]] 2.04Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6g8f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6G8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6G8F FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=K0I:3-[[2-PYRIDIN-2-YL-6-(1,2,4,5-TETRAHYDRO-3-BENZAZEPIN-3-YL)PYRIMIDIN-4-YL]AMINO]PROPANOIC+ACID'>K0I</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6g8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6g8f OCA], [http://pdbe.org/6g8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6g8f RCSB], [http://www.ebi.ac.uk/pdbsum/6g8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6g8f ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/KDM6A_HUMAN KDM6A_HUMAN]] Kabuki syndrome. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM6A_HUMAN KDM6A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-27'. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Demethylation of 'Lys-27' of histone H3 is concomitant with methylation of 'Lys-4' of histone H3, and regulates the recruitment of the PRC1 complex and monoubiquitination of histone H2A.<ref>PMID:17851529</ref> <ref>PMID:17761849</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In the search for new demethylase inhibitors, we have developed a multistep protocol for in silico screening. Millions of poses generated by high-throughput docking or a 3D-pharmacophore search are first minimized by a classical force field and then filtered by semiempirical quantum mechanical calculations of the interaction energy with a selected set of functional groups in the binding site. The final ranking includes solvation effects which are evaluated in the continuum dielectric approximation (finite-difference Poisson equation). Application of the multistep protocol to JMJD3 jumonji demethylase has resulted in a dozen low-micromolar inhibitors belonging to five different chemical classes. We have solved the crystal structure of JMJD3 inhibitor 8 in the complex with UTX (a demethylase in the same subfamily as JMJD3) which validates the predicted binding mode. Compound 8 is a promising candidate for future optimization as it has a favorable ligand efficiency of 0.32 kcal/mol per nonhydrogen atom.

-	~~Authors: Esposito~~, C., ~~Sledz, P.~~, Caflisch, A.	+	In Silico Identification of JMJD3 Demethylase Inhibitors.,Esposito C, Wiedmer L, Caflisch A J Chem Inf Model. 2018 Oct 3. doi: 10.1021/acs.jcim.8b00539. PMID:30226987<ref>PMID:30226987</ref>

-	~~Description: Crystal structure~~ of ~~UTX complexed with GSK-J1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Sledz, P]]~~	+	<div class="pdbe-citations 6g8f" style="background-color:#fffaf0;"></div>
-	~~[[Category: Esposito, C]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Caflisch, A]]		[[Category: Caflisch, A]]
		+	[[Category: Esposito, C]]
		+	[[Category: Sledz, P]]
		+	[[Category: Inhibitor]]
		+	[[Category: Jumonji demethylase]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "6g8f" [edit=sysop:move=sysop]

OCA — Wed, 18 Apr 2018 04:27:58 GMT

Protected "6g8f" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:27, 18 April 2018

OCA: New page: '''Unreleased structure''' The entry 6g8f is ON HOLD Authors: Esposito, C., Sledz, P., Caflisch, A. Description: Crystal structure of UTX complexed with GSK-J1 [[Category: Unreleased S...

OCA — Wed, 18 Apr 2018 04:27:57 GMT

New page: '''Unreleased structure''' The entry 6g8f is ON HOLD Authors: Esposito, C., Sledz, P., Caflisch, A. Description: Crystal structure of UTX complexed with GSK-J1 [[Category: Unreleased S...

New page

'''Unreleased structure'''

The entry 6g8f is ON HOLD

Authors: Esposito, C., Sledz, P., Caflisch, A.

Description: Crystal structure of UTX complexed with GSK-J1
[[Category: Unreleased Structures]]
[[Category: Sledz, P]]
[[Category: Esposito, C]]
[[Category: Caflisch, A]]