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5arf

From Proteopedia

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Current revision

SMYD2 in complex with small molecule inhibitor compound-2

Structural highlights

5arf is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.92Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SMYD2_HUMAN Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Has also methyltransferase activity toward non-histone proteins such as p53/TP53 and RB1. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates 'Lys-860' of RB1/RB.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Protein lysine methyltransferases have recently emerged as a new target class for the development of inhibitors that modulate gene transcription or signaling pathways. SET and MYND domain containing protein 2 (SMYD2) is a catalytic SET domain containing methyltransferase reported to monomethylate lysine residues on histone and nonhistone proteins. Although several studies have uncovered an important role of SMYD2 in promoting cancer by protein methylation, the biology of SMYD2 is far from being fully understood. Utilization of highly potent and selective chemical probes for target validation has emerged as a concept which circumvents possible limitations of knockdown experiments and, in particular, could result in an improved exploration of drug targets with a complex underlying biology. Here, we report the development of a potent, selective, and cell-active, substrate-competitive inhibitor of SMYD2, which is the first reported inhibitor suitable for in vivo target validation studies in rodents.

Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2.,Eggert E, Hillig RC, Koehr S, Stockigt D, Weiske J, Barak N, Mowat J, Brumby T, Christ CD, Ter Laak A, Lang T, Fernandez-Montalvan AE, Badock V, Weinmann H, Hartung IV, Barsyte-Lovejoy D, Szewczyk M, Kennedy S, Li F, Vedadi M, Brown PJ, Santhakumar V, Arrowsmith CH, Stellfeld T, Stresemann C J Med Chem. 2016 May 3. PMID:27075367^[5]

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

References

↑ Huang J, Perez-Burgos L, Placek BJ, Sengupta R, Richter M, Dorsey JA, Kubicek S, Opravil S, Jenuwein T, Berger SL. Repression of p53 activity by Smyd2-mediated methylation. Nature. 2006 Nov 30;444(7119):629-32. Epub 2006 Nov 15. PMID:17108971 doi:10.1038/nature05287
↑ Huang J, Sengupta R, Espejo AB, Lee MG, Dorsey JA, Richter M, Opravil S, Shiekhattar R, Bedford MT, Jenuwein T, Berger SL. p53 is regulated by the lysine demethylase LSD1. Nature. 2007 Sep 6;449(7158):105-8. PMID:17805299 doi:nature06092
↑ Abu-Farha M, Lambert JP, Al-Madhoun AS, Elisma F, Skerjanc IS, Figeys D. The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase. Mol Cell Proteomics. 2008 Mar;7(3):560-72. Epub 2007 Dec 7. PMID:18065756 doi:10.1074/mcp.M700271-MCP200
↑ Saddic LA, West LE, Aslanian A, Yates JR 3rd, Rubin SM, Gozani O, Sage J. Methylation of the retinoblastoma tumor suppressor by SMYD2. J Biol Chem. 2010 Nov 26;285(48):37733-40. doi: 10.1074/jbc.M110.137612. Epub, 2010 Sep 24. PMID:20870719 doi:10.1074/jbc.M110.137612
↑ Eggert E, Hillig RC, Koehr S, Stockigt D, Weiske J, Barak N, Mowat J, Brumby T, Christ CD, Ter Laak A, Lang T, Fernandez-Montalvan AE, Badock V, Weinmann H, Hartung IV, Barsyte-Lovejoy D, Szewczyk M, Kennedy S, Li F, Vedadi M, Brown PJ, Santhakumar V, Arrowsmith CH, Stellfeld T, Stresemann C. Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2. J Med Chem. 2016 May 3. PMID:27075367 doi:http://dx.doi.org/10.1021/acs.jmedchem.5b01890

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/5arf"

@@ Line 1: / Line 1: @@
-==SMYD2 in complex with small molecule inhibitor==
+==SMYD2 in complex with small molecule inhibitor compound-2==
-<StructureSection load='5arf' size='340' side='right' caption='[[5arf]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
+<StructureSection load='5arf' size='340' side='right'caption='[[5arf]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5arf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ARF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ARF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5arf]] is a 1 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=5ARF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ARF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=I9H:N-[3-(4-CHLOROPHENYL)-1-{N-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL}-4,5-DIHYDRO-1H-+PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE'>I9H</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 1.92&#8491;</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=5arf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5arf OCA], [http://pdbe.org/5arf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5arf RCSB], [http://www.ebi.ac.uk/pdbsum/5arf PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=I9H:N-[3-(4-CHLOROPHENYL)-1-{N-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL}-4,5-DIHYDRO-1H-+PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE'>I9H</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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'>[https://proteopedia.org/fgij/fg.htm?mol=5arf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5arf OCA], [https://pdbe.org/5arf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5arf RCSB], [https://www.ebi.ac.uk/pdbsum/5arf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5arf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SMYD2_HUMAN SMYD2_HUMAN]] Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Has also methyltransferase activity toward non-histone proteins such as p53/TP53 and RB1. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates 'Lys-860' of RB1/RB.<ref>PMID:17108971</ref> <ref>PMID:17805299</ref> <ref>PMID:18065756</ref> <ref>PMID:20870719</ref>
+[https://www.uniprot.org/uniprot/SMYD2_HUMAN SMYD2_HUMAN] Protein-lysine N-methyltransferase that methylates both histones and non-histone proteins. Specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). Has also methyltransferase activity toward non-histone proteins such as p53/TP53 and RB1. Monomethylates 'Lys-370' of p53/TP53, leading to decreased DNA-binding activity and subsequent transcriptional regulation activity of p53/TP53. Monomethylates 'Lys-860' of RB1/RB.<ref>PMID:17108971</ref> <ref>PMID:17805299</ref> <ref>PMID:18065756</ref> <ref>PMID:20870719</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5arf" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone methyltransferase 3D structures|Histone methyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Badock, V]]
+[[Category: Homo sapiens]]
-[[Category: Barak, N]]
+[[Category: Large Structures]]
-[[Category: Brumby, T]]
+[[Category: Badock V]]
-[[Category: Christ, C D]]
+[[Category: Barak N]]
-[[Category: Eggert, E]]
+[[Category: Brumby T]]
-[[Category: Fernandez-Montalvan, A E]]
+[[Category: Christ CD]]
-[[Category: Hartung, I V]]
+[[Category: Eggert E]]
-[[Category: Hillig, R C]]
+[[Category: Fernandez-Montalvan AE]]
-[[Category: Koehr, S]]
+[[Category: Hartung IV]]
-[[Category: Laak, A ter]]
+[[Category: Hillig RC]]
-[[Category: Mowat, J]]
+[[Category: Koehr S]]
-[[Category: Mueller, T]]
+[[Category: Mowat J]]
-[[Category: Stellfeld, T]]
+[[Category: Mueller T]]
-[[Category: Stoeckigt, D]]
+[[Category: Stellfeld T]]
-[[Category: Stresemann, C]]
+[[Category: Stoeckigt D]]
-[[Category: Weinmann, H]]
+[[Category: Stresemann C]]
-[[Category: Weiske, J]]
+[[Category: Weinmann H]]
-[[Category: Drug target]]
+[[Category: Weiske J]]
-[[Category: Methyltransferase]]
+[[Category: Ter Laak A]]
-[[Category: Set domain]]
-[[Category: Sgc probe]]
-[[Category: Small molecule inhibitor]]
-[[Category: Transferase]]

5arf

From Proteopedia

Current revision

SMYD2 in complex with small molecule inhibitor compound-2

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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