6cg2: Difference between revisions

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<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
<StructureSection load='6cg2' size='340' side='right' caption='[[6cg2]], [[Resolution|resolution]] 2.34&Aring;' 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>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Human]]
[[Category: Hosfield, D J]]
[[Category: Hosfield, D J]]
[[Category: Nie, Z]]
[[Category: Nie, Z]]

Revision as of 11:33, 2 May 2018

Crystal Structure of KDM4A with Compound 8Crystal Structure of KDM4A with Compound 8

Structural highlights

6cg2 is a 4 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Gene:KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677 (HUMAN)
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.[1] [2] [3] 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.[4] [5] [6]

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.

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[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:http://dx.doi.org/25/15/6404
  2. ↑ Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028
  3. ↑ Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:http://dx.doi.org/10.1371/journal.pgen.1001390
  4. ↑ Zhang D, Yoon HG, Wong J. JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2). Mol Cell Biol. 2005 Aug;25(15):6404-14. PMID:16024779 doi:http://dx.doi.org/25/15/6404
  5. ↑ Whetstine JR, Nottke A, Lan F, Huarte M, Smolikov S, Chen Z, Spooner E, Li E, Zhang G, Colaiacovo M, Shi Y. Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases. Cell. 2006 May 5;125(3):467-81. Epub 2006 Apr 6. PMID:16603238 doi:10.1016/j.cell.2006.03.028
  6. ↑ Verrier L, Escaffit F, Chailleux C, Trouche D, Vandromme M. A new isoform of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation. PLoS Genet. 2011 Jun;7(6):e1001390. doi: 10.1371/journal.pgen.1001390. Epub 2011 , Jun 2. PMID:21694756 doi:http://dx.doi.org/10.1371/journal.pgen.1001390
  7. ↑ Nie Z, Shi L, Lai C, O'Connell SM, Xu J, Stansfield RK, Hosfield DJ, Veal JM, Stafford JA. Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg Med Chem Lett. 2018 Mar 30. pii: S0960-894X(18)30288-9. doi:, 10.1016/j.bmcl.2018.03.083. PMID:29627262 doi:http://dx.doi.org/10.1016/j.bmcl.2018.03.083

6cg2, resolution 2.34Å

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