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'''Unreleased structure'''


The entry 5k72 is ON HOLD  until Paper Publication
==IRAK4 in complex with Compound 21==
<StructureSection load='5k72' size='340' side='right'caption='[[5k72]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5k72]] 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=5K72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K72 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.22&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6QY:~{N}4,~{N}4-dimethyl-~{N}1-[5-(oxan-4-yl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]cyclohexane-1,4-diamine'>6QY</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</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=5k72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k72 OCA], [https://pdbe.org/5k72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k72 RCSB], [https://www.ebi.ac.uk/pdbsum/5k72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k72 ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/IRAK4_HUMAN IRAK4_HUMAN] Defects in IRAK4 are the cause of recurrent isolated invasive pneumococcal disease type 1 (IPD1) [MIM:[https://omim.org/entry/610799 610799]. Recurrent invasive pneumococcal disease (IPD) is defined as two episodes of IPD occurring at least 1 month apart, whether caused by the same or different serotypes or strains. Recurrent IPD occurs in at least 2% of patients in most series, making IPD the most important known risk factor for subsequent IPD.<ref>PMID:16950813</ref>  Defects in IRAK4 are the cause of IRAK4 deficiency (IRAK4D) [MIM:[https://omim.org/entry/607676 607676]. IRAK4 deficiency causes extracellular pyogenic bacterial and fungal infections in otherwise healthy children.<ref>PMID:12925671</ref> <ref>PMID:12637671</ref>
== Function ==
[https://www.uniprot.org/uniprot/IRAK4_HUMAN IRAK4_HUMAN] Serine/threonine-protein kinase that plays a critical role in initiating innate immune response against foreign pathogens. Involved in Toll-like receptor (TLR) and IL-1R signaling pathways. Is rapidly recruited by MYD88 to the receptor-signaling complex upon TLR activation to form the Myddosome together with IRAK2. Phosphorylates initially IRAK1, thus stimulating the kinase activity and intensive autophosphorylation of IRAK1. Phosphorylates E3 ubiquitin ligases Pellino proteins (PELI1, PELI2 and PELI3) to promote pellino-mediated polyubiquitination of IRAK1. Then, the ubiquitin-binding domain of IKBKG/NEMO binds to polyubiquitinated IRAK1 bringing together the IRAK1-MAP3K7/TAK1-TRAF6 complex and the NEMO-IKKA-IKKB complex. In turn, MAP3K7/TAK1 activates IKKs (CHUK/IKKA and IKBKB/IKKB) leading to NF-kappa-B nuclear translocation and activation. Alternatively, phosphorylates TIRAP to promote its ubiquitination and subsequent degradation. Phosphorylates NCF1 and regulates NADPH oxidase activation after LPS stimulation suggesting a similar mechanism during microbial infections.<ref>PMID:11960013</ref> <ref>PMID:12538665</ref> <ref>PMID:15084582</ref> <ref>PMID:17217339</ref> <ref>PMID:17337443</ref> <ref>PMID:17997719</ref> <ref>PMID:20400509</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Herein we report the optimization of a series of pyrrolopyrimidine inhibitors of interleukin-1 receptor associated kinase 4 (IRAK4) using X-ray crystal structures and structure based design to identify and optimize our scaffold. Compound 28 demonstrated a favorable physicochemical and kinase selectivity profile and was identified as a promising in vivo tool with which to explore the role of IRAK4 inhibition in the treatment of mutant MYD88(L265P) diffuse large B-cell lymphoma (DLBCL). Compound 28 was shown to be capable of demonstrating inhibition of NF-kappaB activation and growth of the ABC subtype of DLBCL cell lines in vitro at high concentrations but showed greater effects in combination with a BTK inhibitor at lower concentrations. In vivo, combination of compound 28 and ibrutinib led to tumor regression in an ABC-DLBCL mouse model.


Authors:  
Discovery and Optimisation of Pyrrolopyrimidine Inhibitors of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) for the Treatment of Mutant MYD88(L265P) Diffuse Large B-Cell Lymphoma.,Scott JS, Degorce SL, Anjum R, Culshaw J, Davies RMD, Davies NL, Dillman KS, Dowling JE, Drew L, Ferguson AD, Groombridge SD, Halsall CT, Hudson JA, Lamont S, Lindsay NA, Marden SK, Mayo MF, Pease JE, Perkins DR, Pink JH, Robb GR, Rosen A, Shen M, McWhirter C, Wu D J Med Chem. 2017 Nov 27. doi: 10.1021/acs.jmedchem.7b01290. PMID:29172502<ref>PMID:29172502</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5k72" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Interleukin-1 receptor-associated kinase|Interleukin-1 receptor-associated kinase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Ferguson AD]]

Latest revision as of 12:52, 27 September 2023

IRAK4 in complex with Compound 21IRAK4 in complex with Compound 21

Structural highlights

5k72 is a 4 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 2.22Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

IRAK4_HUMAN Defects in IRAK4 are the cause of recurrent isolated invasive pneumococcal disease type 1 (IPD1) [MIM:610799. Recurrent invasive pneumococcal disease (IPD) is defined as two episodes of IPD occurring at least 1 month apart, whether caused by the same or different serotypes or strains. Recurrent IPD occurs in at least 2% of patients in most series, making IPD the most important known risk factor for subsequent IPD.[1] Defects in IRAK4 are the cause of IRAK4 deficiency (IRAK4D) [MIM:607676. IRAK4 deficiency causes extracellular pyogenic bacterial and fungal infections in otherwise healthy children.[2] [3]

Function

IRAK4_HUMAN Serine/threonine-protein kinase that plays a critical role in initiating innate immune response against foreign pathogens. Involved in Toll-like receptor (TLR) and IL-1R signaling pathways. Is rapidly recruited by MYD88 to the receptor-signaling complex upon TLR activation to form the Myddosome together with IRAK2. Phosphorylates initially IRAK1, thus stimulating the kinase activity and intensive autophosphorylation of IRAK1. Phosphorylates E3 ubiquitin ligases Pellino proteins (PELI1, PELI2 and PELI3) to promote pellino-mediated polyubiquitination of IRAK1. Then, the ubiquitin-binding domain of IKBKG/NEMO binds to polyubiquitinated IRAK1 bringing together the IRAK1-MAP3K7/TAK1-TRAF6 complex and the NEMO-IKKA-IKKB complex. In turn, MAP3K7/TAK1 activates IKKs (CHUK/IKKA and IKBKB/IKKB) leading to NF-kappa-B nuclear translocation and activation. Alternatively, phosphorylates TIRAP to promote its ubiquitination and subsequent degradation. Phosphorylates NCF1 and regulates NADPH oxidase activation after LPS stimulation suggesting a similar mechanism during microbial infections.[4] [5] [6] [7] [8] [9] [10]

Publication Abstract from PubMed

Herein we report the optimization of a series of pyrrolopyrimidine inhibitors of interleukin-1 receptor associated kinase 4 (IRAK4) using X-ray crystal structures and structure based design to identify and optimize our scaffold. Compound 28 demonstrated a favorable physicochemical and kinase selectivity profile and was identified as a promising in vivo tool with which to explore the role of IRAK4 inhibition in the treatment of mutant MYD88(L265P) diffuse large B-cell lymphoma (DLBCL). Compound 28 was shown to be capable of demonstrating inhibition of NF-kappaB activation and growth of the ABC subtype of DLBCL cell lines in vitro at high concentrations but showed greater effects in combination with a BTK inhibitor at lower concentrations. In vivo, combination of compound 28 and ibrutinib led to tumor regression in an ABC-DLBCL mouse model.

Discovery and Optimisation of Pyrrolopyrimidine Inhibitors of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) for the Treatment of Mutant MYD88(L265P) Diffuse Large B-Cell Lymphoma.,Scott JS, Degorce SL, Anjum R, Culshaw J, Davies RMD, Davies NL, Dillman KS, Dowling JE, Drew L, Ferguson AD, Groombridge SD, Halsall CT, Hudson JA, Lamont S, Lindsay NA, Marden SK, Mayo MF, Pease JE, Perkins DR, Pink JH, Robb GR, Rosen A, Shen M, McWhirter C, Wu D J Med Chem. 2017 Nov 27. doi: 10.1021/acs.jmedchem.7b01290. PMID:29172502[11]

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

See Also

References

  1. ↑ Ku CL, Picard C, Erdos M, Jeurissen A, Bustamante J, Puel A, von Bernuth H, Filipe-Santos O, Chang HH, Lawrence T, Raes M, Marodi L, Bossuyt X, Casanova JL. IRAK4 and NEMO mutations in otherwise healthy children with recurrent invasive pneumococcal disease. J Med Genet. 2007 Jan;44(1):16-23. Epub 2006 Sep 1. PMID:16950813 doi:jmg.2006.044446
  2. ↑ Medvedev AE, Lentschat A, Kuhns DB, Blanco JC, Salkowski C, Zhang S, Arditi M, Gallin JI, Vogel SN. Distinct mutations in IRAK-4 confer hyporesponsiveness to lipopolysaccharide and interleukin-1 in a patient with recurrent bacterial infections. J Exp Med. 2003 Aug 18;198(4):521-31. PMID:12925671 doi:http://dx.doi.org/10.1084/jem.20030701
  3. ↑ Picard C, Puel A, Bonnet M, Ku CL, Bustamante J, Yang K, Soudais C, Dupuis S, Feinberg J, Fieschi C, Elbim C, Hitchcock R, Lammas D, Davies G, Al-Ghonaium A, Al-Rayes H, Al-Jumaah S, Al-Hajjar S, Al-Mohsen IZ, Frayha HH, Rucker R, Hawn TR, Aderem A, Tufenkeji H, Haraguchi S, Day NK, Good RA, Gougerot-Pocidalo MA, Ozinsky A, Casanova JL. Pyogenic bacterial infections in humans with IRAK-4 deficiency. Science. 2003 Mar 28;299(5615):2076-9. Epub 2003 Mar 13. PMID:12637671 doi:10.1126/science.1081902
  4. ↑ Li S, Strelow A, Fontana EJ, Wesche H. IRAK-4: a novel member of the IRAK family with the properties of an IRAK-kinase. Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5567-72. PMID:11960013 doi:10.1073/pnas.082100399
  5. ↑ Burns K, Janssens S, Brissoni B, Olivos N, Beyaert R, Tschopp J. Inhibition of interleukin 1 receptor/Toll-like receptor signaling through the alternatively spliced, short form of MyD88 is due to its failure to recruit IRAK-4. J Exp Med. 2003 Jan 20;197(2):263-8. PMID:12538665
  6. ↑ Qin J, Jiang Z, Qian Y, Casanova JL, Li X. IRAK4 kinase activity is redundant for interleukin-1 (IL-1) receptor-associated kinase phosphorylation and IL-1 responsiveness. J Biol Chem. 2004 Jun 18;279(25):26748-53. Epub 2004 Apr 14. PMID:15084582 doi:10.1074/jbc.M400785200
  7. ↑ Pacquelet S, Johnson JL, Ellis BA, Brzezinska AA, Lane WS, Munafo DB, Catz SD. Cross-talk between IRAK-4 and the NADPH oxidase. Biochem J. 2007 May 1;403(3):451-61. PMID:17217339 doi:10.1042/BJ20061184
  8. ↑ Koziczak-Holbro M, Joyce C, Gluck A, Kinzel B, Muller M, Tschopp C, Mathison JC, Davis CN, Gram H. IRAK-4 kinase activity is required for interleukin-1 (IL-1) receptor- and toll-like receptor 7-mediated signaling and gene expression. J Biol Chem. 2007 May 4;282(18):13552-60. Epub 2007 Mar 2. PMID:17337443 doi:10.1074/jbc.M700548200
  9. ↑ Ordureau A, Smith H, Windheim M, Peggie M, Carrick E, Morrice N, Cohen P. The IRAK-catalysed activation of the E3 ligase function of Pellino isoforms induces the Lys63-linked polyubiquitination of IRAK1. Biochem J. 2008 Jan 1;409(1):43-52. PMID:17997719 doi:10.1042/BJ20071365
  10. ↑ Dunne A, Carpenter S, Brikos C, Gray P, Strelow A, Wesche H, Morrice N, O'Neill LA. IRAK1 and IRAK4 promote phosphorylation, ubiquitination, and degradation of MyD88 adaptor-like (Mal). J Biol Chem. 2010 Jun 11;285(24):18276-82. doi: 10.1074/jbc.M109.098137. Epub, 2010 Apr 16. PMID:20400509 doi:10.1074/jbc.M109.098137
  11. ↑ Scott JS, Degorce SL, Anjum R, Culshaw J, Davies RMD, Davies NL, Dillman KS, Dowling JE, Drew L, Ferguson AD, Groombridge SD, Halsall CT, Hudson JA, Lamont S, Lindsay NA, Marden SK, Mayo MF, Pease JE, Perkins DR, Pink JH, Robb GR, Rosen A, Shen M, McWhirter C, Wu D. Discovery and Optimisation of Pyrrolopyrimidine Inhibitors of Interleukin-1 Receptor Associated Kinase 4 (IRAK4) for the Treatment of Mutant MYD88(L265P) Diffuse Large B-Cell Lymphoma. J Med Chem. 2017 Nov 27. doi: 10.1021/acs.jmedchem.7b01290. PMID:29172502 doi:http://dx.doi.org/10.1021/acs.jmedchem.7b01290

5k72, resolution 2.22Å

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