6cg2 - Revision history

OCA at 15:04, 4 October 2023

OCA — Wed, 04 Oct 2023 15:04:05 GMT

←Older revision		Revision as of 15:04, 4 October 2023
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	==Crystal Structure of KDM4A with Compound 8==		==Crystal Structure of KDM4A with Compound 8==
-	<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution\|resolution]] 2.34Å' scene=''>	+	<StructureSection load='6cg2' size='340' side='right'caption='[[6cg2]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cg2]] 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=6CG2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cg2]] 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=6CG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CG2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=QC2:2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic+acid'>QC2</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]] 2.34Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 ([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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=QC2:2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic+acid'>QC2</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=6cg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cg2 OCA], [~~http~~://pdbe.org/6cg2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cg2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cg2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cg2 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=6cg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cg2 OCA], [https://pdbe.org/6cg2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cg2 RCSB], [https://www.ebi.ac.uk/pdbsum/6cg2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cg2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>	+	[https://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6cg2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cg2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Jumonji domain-containing protein 3D structures\|Jumonji domain-containing protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Hosfield, D J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nie, Z~~]]	+	[[Category: Hosfield DJ]]
-	[[Category: ~~Demethylase]]~~	+	[[Category: Nie Z]]
-	~~[[Category: Kdm4a]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxidoreductase-inhibitor complex]]~~	+
-	~~[[Category: Small molecule inhibitor~~]]	+

OCA at 08:33, 2 May 2018

OCA — Wed, 02 May 2018 08:33:04 GMT

←Older revision		Revision as of 08:33, 2 May 2018
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	<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution\|resolution]] 2.34Å' scene=''>		<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution\|resolution]] 2.34Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cg2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CG2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cg2]] 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=6CG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CG2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=QC2:2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic+acid'>QC2</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=QC2:2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic+acid'>QC2</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">KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 ([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=6cg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cg2 OCA], [http://pdbe.org/6cg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cg2 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=6cg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cg2 OCA], [http://pdbe.org/6cg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cg2 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Hosfield, D J]]		[[Category: Hosfield, D J]]
	[[Category: Nie, Z]]		[[Category: Nie, Z]]

OCA at 05:45, 18 April 2018

OCA — Wed, 18 Apr 2018 05:45:14 GMT

←Older revision		Revision as of 05:45, 18 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6cg2 is ~~ON HOLD~~	+	==Crystal Structure of KDM4A with Compound 8==
		+	<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution\|resolution]] 2.34Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6cg2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CG2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CG2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=QC2:2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic+acid'>QC2</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=6cg2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cg2 OCA], [http://pdbe.org/6cg2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cg2 RCSB], [http://www.ebi.ac.uk/pdbsum/6cg2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cg2 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KDM4A_HUMAN KDM4A_HUMAN]] Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref> Isoform 2: Crucial for muscle differentiation, promotes transcriptional activation of the Myog gene by directing the removal of repressive chromatin marks at its promoter. Lacks the N-terminal demethylase domain.<ref>PMID:16024779</ref> <ref>PMID:16603238</ref> <ref>PMID:21694756</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Histone lysine demethylases (KDMs) play a key role in epigenetic regulation and KDM5A and KDM5B have been identified as potential anti-cancer drug targets. Using structural information from known KDM4 and KDM5 inhibitors, a potent series of pyrazolylpyridines was designed. Structure-activity relationship (SAR) exploration resulted in the identification of compound 33, an orally available, potent inhibitor of KDM5A/5B with promising selectivity. Potent cellular inhibition as measured by levels of tri-methylated H3K4 was demonstrated with compound 33 in the breast cancer cell line ZR-75-1.

-	~~Authors:~~ Hosfield, D.J., ~~Nie, Z~~.	+	Structure-based design and discovery of potent and selective KDM5 inhibitors.,Nie Z, Shi L, Lai C, O'Connell SM, Xu J, Stansfield RK, Hosfield DJ, Veal JM, Stafford JA Bioorg Med Chem Lett. 2018 Mar 30. pii: S0960-894X(18)30288-9. doi:, 10.1016/j.bmcl.2018.03.083. PMID:29627262<ref>PMID:29627262</ref>

-	~~Description: Crystal Structure~~ of ~~KDM4A with Compound 8~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: Hosfield, D.J]]	+	<div class="pdbe-citations 6cg2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hosfield, D J]]
	[[Category: Nie, Z]]		[[Category: Nie, Z]]
		+	[[Category: Demethylase]]
		+	[[Category: Kdm4a]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Oxidoreductase-inhibitor complex]]
		+	[[Category: Small molecule inhibitor]]

OCA: Protected "6cg2" [edit=sysop:move=sysop]

OCA — Wed, 28 Feb 2018 05:02:35 GMT

Protected "6cg2" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:02, 28 February 2018

OCA: New page: '''Unreleased structure''' The entry 6cg2 is ON HOLD Authors: Hosfield, D.J., Nie, Z. Description: Crystal Structure of KDM4A with Compound 8 Category: Unreleased Structures [[Cate...

OCA — Wed, 28 Feb 2018 05:02:34 GMT

New page: '''Unreleased structure''' The entry 6cg2 is ON HOLD Authors: Hosfield, D.J., Nie, Z. Description: Crystal Structure of KDM4A with Compound 8 Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 6cg2 is ON HOLD

Authors: Hosfield, D.J., Nie, Z.

Description: Crystal Structure of KDM4A with Compound 8
[[Category: Unreleased Structures]]
[[Category: Hosfield, D.J]]
[[Category: Nie, Z]]