This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5u5h

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:27, 23 September 2020

Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine

Structural highlights

5u5h is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	5u5k, 5u62, 5u5t
Gene:	EED (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[EED_HUMAN] Polycomb group (PcG) protein. Component of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' and 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. Also recognizes 'Lys-26' trimethylated histone H1 with the effect of inhibiting PRC2 complex methyltransferase activity on nucleosomal histone H3 'Lys-27', whereas H3 'Lys-27' recognition has the opposite effect, enabling the propagation of this repressive mark. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. Genes repressed by the PRC2/EED-EZH2 complex include HOXC8, HOXA9, MYT1 and CDKN2A.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in antitumor efficacy. Here, we describe the optimization of a chemical series representing a new class of PRC2 inhibitors which acts allosterically via the trimethyllysine pocket of the noncatalytic EED subunit. Deconstruction of a larger and complex screening hit to a simple fragment-sized molecule followed by structure-guided regrowth and careful property modulation were employed to yield compounds which achieve submicromolar inhibition in functional assays and cellular activity. The resulting molecules can serve as a simplified entry point for lead optimization and can be utilized to study this new mechanism of PRC2 inhibition and the associated biology in detail.

Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.,Lingel A, Sendzik M, Huang Y, Shultz MD, Cantwell J, Dillon MP, Fu X, Fuller J, Gabriel T, Gu J, Jiang X, Li L, Liang F, McKenna M, Qi W, Rao W, Sheng X, Shu W, Sutton J, Taft B, Wang L, Zeng J, Zhang H, Zhang M, Zhao K, Lindvall M, Bussiere DE J Med Chem. 2017 Jan 12;60(1):415-427. doi: 10.1021/acs.jmedchem.6b01473. Epub, 2017 Jan 3. PMID:27992714^[10]

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

References

↑ Sewalt RG, van der Vlag J, Gunster MJ, Hamer KM, den Blaauwen JL, Satijn DP, Hendrix T, van Driel R, Otte AP. Characterization of interactions between the mammalian polycomb-group proteins Enx1/EZH2 and EED suggests the existence of different mammalian polycomb-group protein complexes. Mol Cell Biol. 1998 Jun;18(6):3586-95. PMID:9584199
↑ van der Vlag J, Otte AP. Transcriptional repression mediated by the human polycomb-group protein EED involves histone deacetylation. Nat Genet. 1999 Dec;23(4):474-8. PMID:10581039 doi:10.1038/70602
↑ Bracken AP, Pasini D, Capra M, Prosperini E, Colli E, Helin K. EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer. EMBO J. 2003 Oct 15;22(20):5323-35. PMID:14532106 doi:10.1093/emboj/cdg542
↑ Pasini D, Bracken AP, Jensen MR, Lazzerini Denchi E, Helin K. Suz12 is essential for mouse development and for EZH2 histone methyltransferase activity. EMBO J. 2004 Oct 13;23(20):4061-71. Epub 2004 Sep 23. PMID:15385962 doi:10.1038/sj.emboj.7600402
↑ Kirmizis A, Bartley SM, Kuzmichev A, Margueron R, Reinberg D, Green R, Farnham PJ. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 2004 Jul 1;18(13):1592-605. PMID:15231737 doi:10.1101/gad.1200204
↑ Cao R, Zhang Y. SUZ12 is required for both the histone methyltransferase activity and the silencing function of the EED-EZH2 complex. Mol Cell. 2004 Jul 2;15(1):57-67. PMID:15225548 doi:10.1016/j.molcel.2004.06.020
↑ Vire E, Brenner C, Deplus R, Blanchon L, Fraga M, Didelot C, Morey L, Van Eynde A, Bernard D, Vanderwinden JM, Bollen M, Esteller M, Di Croce L, de Launoit Y, Fuks F. The Polycomb group protein EZH2 directly controls DNA methylation. Nature. 2006 Feb 16;439(7078):871-4. Epub 2005 Dec 14. PMID:16357870 doi:10.1038/nature04431
↑ Sarma K, Margueron R, Ivanov A, Pirrotta V, Reinberg D. Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol Cell Biol. 2008 Apr;28(8):2718-31. doi: 10.1128/MCB.02017-07. Epub 2008 Feb, 19. PMID:18285464 doi:10.1128/MCB.02017-07
↑ Xu C, Bian C, Yang W, Galka M, Ouyang H, Chen C, Qiu W, Liu H, Jones AE, Mackenzie F, Pan P, Li SS, Wang H, Min J. Binding of different histone marks differentially regulates the activity and specificity of polycomb repressive complex 2 (PRC2). Proc Natl Acad Sci U S A. 2010 Oct 25. PMID:20974918 doi:10.1073/pnas.1008937107
↑ Lingel A, Sendzik M, Huang Y, Shultz MD, Cantwell J, Dillon MP, Fu X, Fuller J, Gabriel T, Gu J, Jiang X, Li L, Liang F, McKenna M, Qi W, Rao W, Sheng X, Shu W, Sutton J, Taft B, Wang L, Zeng J, Zhang H, Zhang M, Zhao K, Lindvall M, Bussiere DE. Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase. J Med Chem. 2017 Jan 12;60(1):415-427. doi: 10.1021/acs.jmedchem.6b01473. Epub, 2017 Jan 3. PMID:27992714 doi:http://dx.doi.org/10.1021/acs.jmedchem.6b01473

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5u5h"

@@ Line 1: / Line 1: @@
 ==Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine==
-<StructureSection load='5u5h' size='340' side='right' caption='[[5u5h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='5u5h' size='340' side='right'caption='[[5u5h]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5u5h]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U5H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U5H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5u5h]] 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=5U5H OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5U5H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7VV:(6S)-6-[(2-FLUORO-5-METHOXYPHENYL)METHYL]-1-(PROPAN-2-YL)-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE'>7VV</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7VV:(6S)-6-[(2-FLUORO-5-METHOXYPHENYL)METHYL]-1-(PROPAN-2-YL)-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE'>7VV</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5u5k|5u5k]], [[5u62|5u62]], [[5u5t|5u5t]]</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=5u5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5h OCA], [http://pdbe.org/5u5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u5h RCSB], [http://www.ebi.ac.uk/pdbsum/5u5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5h ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EED ([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://proteopedia.org/fgij/fg.htm?mol=5u5h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u5h OCA], [http://pdbe.org/5u5h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u5h RCSB], [http://www.ebi.ac.uk/pdbsum/5u5h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u5h ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 </div>
 <div class="pdbe-citations 5u5h" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Polycomb|Polycomb]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Bussiere, D]]
 [[Category: Shu, W]]

5u5h

From Proteopedia

Revision as of 12:27, 23 September 2020

Crystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox