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'''Unreleased structure'''


The entry 6nfi is ON HOLD  until Paper Publication
==BTK in complex with inhibitor N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamide==
<StructureSection load='6nfi' size='340' side='right'caption='[[6nfi]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6nfi]] 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=6NFI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NFI 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]] 2.41&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KLP:N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamide'>KLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6nfi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfi OCA], [https://pdbe.org/6nfi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nfi RCSB], [https://www.ebi.ac.uk/pdbsum/6nfi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfi ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/BTK_HUMAN BTK_HUMAN] Defects in BTK are the cause of X-linked agammaglobulinemia (XLA) [MIM:[https://omim.org/entry/300755 300755]; also known as X-linked agammaglobulinemia type 1 (AGMX1) or immunodeficiency type 1 (IMD1). XLA is a humoral immunodeficiency disease which results in developmental defects in the maturation pathway of B-cells. Affected boys have normal levels of pre-B-cells in their bone marrow but virtually no circulating mature B-lymphocytes. This results in a lack of immunoglobulins of all classes and leads to recurrent bacterial infections like otitis, conjunctivitis, dermatitis, sinusitis in the first few years of life, or even some patients present overwhelming sepsis or meningitis, resulting in death in a few hours. Treatment in most cases is by infusion of intravenous immunoglobulin.<ref>PMID:7880320</ref> <ref>PMID:8013627</ref> <ref>PMID:8162056</ref> <ref>PMID:8162018</ref> <ref>PMID:7849697</ref> <ref>PMID:7849721</ref> <ref>PMID:7809124</ref> <ref>PMID:7849006</ref> <ref>PMID:7711734</ref> <ref>PMID:7633420</ref> <ref>PMID:7633429</ref> <ref>PMID:8634718</ref> <ref>PMID:7627183</ref> <ref>PMID:7897635</ref> <ref>PMID:8723128</ref> <ref>PMID:8695804</ref> <ref>PMID:8834236</ref> <ref>PMID:9280283</ref> <ref>PMID:9260159</ref> <ref>PMID:9545398</ref> <ref>PMID:9445504</ref> <ref>PMID:10220140</ref> <ref>PMID:10678660</ref> <ref>PMID:10612838</ref>  Defects in BTK may be the cause of X-linked hypogammaglobulinemia and isolated growth hormone deficiency (XLA-IGHD) [MIM:[https://omim.org/entry/307200 307200]; also known as agammaglobulinemia and isolated growth hormone deficiency or Fleisher syndrome or isolated growth hormone deficiency type 3 (IGHD3). In rare cases XLA is inherited together with isolated growth hormone deficiency (IGHD).
== Function ==
[https://www.uniprot.org/uniprot/BTK_HUMAN BTK_HUMAN] Non-receptor tyrosine kinase indispensable for B lymphocyte development, differentiation and signaling. Binding of antigen to the B-cell antigen receptor (BCR) triggers signaling that ultimately leads to B-cell activation. After BCR engagement and activation at the plasma membrane, phosphorylates PLCG2 at several sites, igniting the downstream signaling pathway through calcium mobilization, followed by activation of the protein kinase C (PKC) family members. PLCG2 phosphorylation is performed in close cooperation with the adapter protein B-cell linker protein BLNK. BTK acts as a platform to bring together a diverse array of signaling proteins and is implicated in cytokine receptor signaling pathways. Plays an important role in the function of immune cells of innate as well as adaptive immunity, as a component of the Toll-like receptors (TLR) pathway. The TLR pathway acts as a primary surveillance system for the detection of pathogens and are crucial to the activation of host defense. Especially, is a critical molecule in regulating TLR9 activation in splenic B-cells. Within the TLR pathway, induces tyrosine phosphorylation of TIRAP which leads to TIRAP degradation. BTK plays also a critical role in transcription regulation. Induces the activity of NF-kappa-B, which is involved in regulating the expression of hundreds of genes. BTK is involved on the signaling pathway linking TLR8 and TLR9 to NF-kappa-B. Transiently phosphorylates transcription factor GTF2I on tyrosine residues in response to BCR. GTF2I then translocates to the nucleus to bind regulatory enhancer elements to modulate gene expression. ARID3A and NFAT are other transcriptional target of BTK. BTK is required for the formation of functional ARID3A DNA-binding complexes. There is however no evidence that BTK itself binds directly to DNA. BTK has a dual role in the regulation of apoptosis.<ref>PMID:9012831</ref> <ref>PMID:11606584</ref> <ref>PMID:16517732</ref> <ref>PMID:16738337</ref> <ref>PMID:16415872</ref> <ref>PMID:17932028</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
At the onset of a drug discovery program, the goal is to identify novel compounds with appropriate chemical features that can be taken forward as lead series. Here, we describe three prospective case studies, Bruton Tyrosine Kinase (BTK), RAR-Related Orphan Receptor gamma t (RORgammat) and Human Leukocyte Antigen DR isotype (HLA-DR) to illustrate the positive impact of high throughput virtual screening (HTVS) on the successful identification of novel chemical series. Each case represents a project with a varying degree of difficulty due to the amount of structural and ligand information available internally or in the public domain to utilize in the virtual screens. We show that HTVS can be effectively employed to identify a diverse set of potent hits for each protein system even when the gold standard, high resolution structural data or ligand binding data for benchmarking is not available.


Authors:  
Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry.,Damm-Ganamet KL, Arora N, Becart S, Edwards JP, Lebsack AD, McAllister H, Nelen MI, Rao N, Westover L, Wiener JJM, Mirzadegan T J Chem Inf Model. 2019 Feb 28. doi: 10.1021/acs.jcim.8b00941. PMID:30817167<ref>PMID:30817167</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 6nfi" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Tyrosine kinase 3D structures|Tyrosine kinase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Damm-Ganamet KL]]
[[Category: Mirzadegan T]]

Latest revision as of 09:52, 11 October 2023

BTK in complex with inhibitor N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamideBTK in complex with inhibitor N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamide

Structural highlights

6nfi 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 2.41Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

BTK_HUMAN Defects in BTK are the cause of X-linked agammaglobulinemia (XLA) [MIM:300755; also known as X-linked agammaglobulinemia type 1 (AGMX1) or immunodeficiency type 1 (IMD1). XLA is a humoral immunodeficiency disease which results in developmental defects in the maturation pathway of B-cells. Affected boys have normal levels of pre-B-cells in their bone marrow but virtually no circulating mature B-lymphocytes. This results in a lack of immunoglobulins of all classes and leads to recurrent bacterial infections like otitis, conjunctivitis, dermatitis, sinusitis in the first few years of life, or even some patients present overwhelming sepsis or meningitis, resulting in death in a few hours. Treatment in most cases is by infusion of intravenous immunoglobulin.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] Defects in BTK may be the cause of X-linked hypogammaglobulinemia and isolated growth hormone deficiency (XLA-IGHD) [MIM:307200; also known as agammaglobulinemia and isolated growth hormone deficiency or Fleisher syndrome or isolated growth hormone deficiency type 3 (IGHD3). In rare cases XLA is inherited together with isolated growth hormone deficiency (IGHD).

Function

BTK_HUMAN Non-receptor tyrosine kinase indispensable for B lymphocyte development, differentiation and signaling. Binding of antigen to the B-cell antigen receptor (BCR) triggers signaling that ultimately leads to B-cell activation. After BCR engagement and activation at the plasma membrane, phosphorylates PLCG2 at several sites, igniting the downstream signaling pathway through calcium mobilization, followed by activation of the protein kinase C (PKC) family members. PLCG2 phosphorylation is performed in close cooperation with the adapter protein B-cell linker protein BLNK. BTK acts as a platform to bring together a diverse array of signaling proteins and is implicated in cytokine receptor signaling pathways. Plays an important role in the function of immune cells of innate as well as adaptive immunity, as a component of the Toll-like receptors (TLR) pathway. The TLR pathway acts as a primary surveillance system for the detection of pathogens and are crucial to the activation of host defense. Especially, is a critical molecule in regulating TLR9 activation in splenic B-cells. Within the TLR pathway, induces tyrosine phosphorylation of TIRAP which leads to TIRAP degradation. BTK plays also a critical role in transcription regulation. Induces the activity of NF-kappa-B, which is involved in regulating the expression of hundreds of genes. BTK is involved on the signaling pathway linking TLR8 and TLR9 to NF-kappa-B. Transiently phosphorylates transcription factor GTF2I on tyrosine residues in response to BCR. GTF2I then translocates to the nucleus to bind regulatory enhancer elements to modulate gene expression. ARID3A and NFAT are other transcriptional target of BTK. BTK is required for the formation of functional ARID3A DNA-binding complexes. There is however no evidence that BTK itself binds directly to DNA. BTK has a dual role in the regulation of apoptosis.[25] [26] [27] [28] [29] [30]

Publication Abstract from PubMed

At the onset of a drug discovery program, the goal is to identify novel compounds with appropriate chemical features that can be taken forward as lead series. Here, we describe three prospective case studies, Bruton Tyrosine Kinase (BTK), RAR-Related Orphan Receptor gamma t (RORgammat) and Human Leukocyte Antigen DR isotype (HLA-DR) to illustrate the positive impact of high throughput virtual screening (HTVS) on the successful identification of novel chemical series. Each case represents a project with a varying degree of difficulty due to the amount of structural and ligand information available internally or in the public domain to utilize in the virtual screens. We show that HTVS can be effectively employed to identify a diverse set of potent hits for each protein system even when the gold standard, high resolution structural data or ligand binding data for benchmarking is not available.

Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry.,Damm-Ganamet KL, Arora N, Becart S, Edwards JP, Lebsack AD, McAllister H, Nelen MI, Rao N, Westover L, Wiener JJM, Mirzadegan T J Chem Inf Model. 2019 Feb 28. doi: 10.1021/acs.jcim.8b00941. PMID:30817167[31]

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

See Also

References

  1. ↑ Hagemann TL, Chen Y, Rosen FS, Kwan SP. Genomic organization of the Btk gene and exon scanning for mutations in patients with X-linked agammaglobulinemia. Hum Mol Genet. 1994 Oct;3(10):1743-9. PMID:7880320
  2. ↑ Duriez B, Duquesnoy P, Dastot F, Bougneres P, Amselem S, Goossens M. An exon-skipping mutation in the btk gene of a patient with X-linked agammaglobulinemia and isolated growth hormone deficiency. FEBS Lett. 1994 Jun 13;346(2-3):165-70. PMID:8013627
  3. ↑ Bradley LA, Sweatman AK, Lovering RC, Jones AM, Morgan G, Levinsky RJ, Kinnon C. Mutation detection in the X-linked agammaglobulinemia gene, BTK, using single strand conformation polymorphism analysis. Hum Mol Genet. 1994 Jan;3(1):79-83. PMID:8162056
  4. ↑ de Weers M, Mensink RG, Kraakman ME, Schuurman RK, Hendriks RW. Mutation analysis of the Bruton's tyrosine kinase gene in X-linked agammaglobulinemia: identification of a mutation which affects the same codon as is altered in immunodeficient xid mice. Hum Mol Genet. 1994 Jan;3(1):161-6. PMID:8162018
  5. ↑ Conley ME, Fitch-Hilgenberg ME, Cleveland JL, Parolini O, Rohrer J. Screening of genomic DNA to identify mutations in the gene for Bruton's tyrosine kinase. Hum Mol Genet. 1994 Oct;3(10):1751-6. PMID:7849697
  6. ↑ Zhu Q, Zhang M, Winkelstein J, Chen SH, Ochs HD. Unique mutations of Bruton's tyrosine kinase in fourteen unrelated X-linked agammaglobulinemia families. Hum Mol Genet. 1994 Oct;3(10):1899-900. PMID:7849721
  7. ↑ Vihinen M, Vetrie D, Maniar HS, Ochs HD, Zhu Q, Vorechovsky I, Webster AD, Notarangelo LD, Nilsson L, Sowadski JM, et al.. Structural basis for chromosome X-linked agammaglobulinemia: a tyrosine kinase disease. Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12803-7. PMID:7809124
  8. ↑ Vihinen M, Zvelebil MJ, Zhu Q, Brooimans RA, Ochs HD, Zegers BJ, Nilsson L, Waterfield MD, Smith CI. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry. 1995 Feb 7;34(5):1475-81. PMID:7849006
  9. ↑ Vorechovsky I, Vihinen M, de Saint Basile G, Honsova S, Hammarstrom L, Muller S, Nilsson L, Fischer A, Smith CI. DNA-based mutation analysis of Bruton's tyrosine kinase gene in patients with X-linked agammaglobulinaemia. Hum Mol Genet. 1995 Jan;4(1):51-8. PMID:7711734
  10. ↑ Jin H, Webster AD, Vihinen M, Sideras P, Vorechovsky I, Hammarstrom L, Bernatowska-Matuszkiewicz E, Smith CI, Bobrow M, Vetrie D. Identification of Btk mutations in 20 unrelated patients with X-linked agammaglobulinaemia (XLA). Hum Mol Genet. 1995 Apr;4(4):693-700. PMID:7633420
  11. ↑ Gaspar HB, Bradley LA, Katz F, Lovering RC, Roifman CM, Morgan G, Levinsky RJ, Kinnon C. Mutation analysis in Bruton's tyrosine kinase, the X-linked agammaglobulinaemia gene, including identification of an insertional hotspot. Hum Mol Genet. 1995 Apr;4(4):755-7. PMID:7633429
  12. ↑ Vorechovsky I, Luo L, de Saint Basile G, Hammarstrom L, Webster AD, Smith CI. Improved oligonucleotide primer set for molecular diagnosis of X-linked agammaglobulinaemia: predominance of amino acid substitutions in the catalytic domain of Bruton's tyrosine kinase. Hum Mol Genet. 1995 Dec;4(12):2403-5. PMID:8634718
  13. ↑ Hagemann TL, Rosen FS, Kwan SP. Characterization of germline mutations of the gene encoding Bruton's tyrosine kinase in families with X-linked agammaglobulinemia. Hum Mutat. 1995;5(4):296-302. PMID:7627183 doi:http://dx.doi.org/10.1002/humu.1380050405
  14. ↑ Ohashi Y, Tsuchiya S, Konno T. A new point mutation involving a highly conserved leucine in the Btk SH2 domain in a family with X linked agammaglobulinaemia. J Med Genet. 1995 Jan;32(1):77-8. PMID:7897635
  15. ↑ Schuster V, Seidenspinner S, Kreth HW. Detection of a novel mutation in the SRC homology domain 2 (SH2) of Bruton's tyrosine kinase and direct female carrier evaluation in a family with X-linked agammaglobulinemia. Am J Med Genet. 1996 May 3;63(1):318-22. PMID:8723128 doi:<318::AID-AJMG53>3.0.CO;2-N 10.1002/(SICI)1096-8628(19960503)63:1<318::AID-AJMG53>3.0.CO;2-N
  16. ↑ Hashimoto S, Tsukada S, Matsushita M, Miyawaki T, Niida Y, Yachie A, Kobayashi S, Iwata T, Hayakawa H, Matsuoka H, Tsuge I, Yamadori T, Kunikata T, Arai S, Yoshizaki K, Taniguchi N, Kishimoto T. Identification of Bruton's tyrosine kinase (Btk) gene mutations and characterization of the derived proteins in 35 X-linked agammaglobulinemia families: a nationwide study of Btk deficiency in Japan. Blood. 1996 Jul 15;88(2):561-73. PMID:8695804
  17. ↑ Kobayashi S, Iwata T, Saito M, Iwasaki R, Matsumoto H, Naritaka S, Kono Y, Hayashi Y. Mutations of the Btk gene in 12 unrelated families with X-linked agammaglobulinemia in Japan. Hum Genet. 1996 Apr;97(4):424-30. PMID:8834236
  18. ↑ Vihinen M, Nore BF, Mattsson PT, Backesjo CM, Nars M, Koutaniemi S, Watanabe C, Lester T, Jones A, Ochs HD, Smith CI. Missense mutations affecting a conserved cysteine pair in the TH domain of Btk. FEBS Lett. 1997 Aug 18;413(2):205-10. PMID:9280283
  19. ↑ Saha BK, Curtis SK, Vogler LB, Vihinen M. Molecular and structural characterization of five novel mutations in the Bruton's tyrosine kinase gene from patients with X-linked agammaglobulinemia. Mol Med. 1997 Jul;3(7):477-85. PMID:9260159
  20. ↑ Conley ME, Mathias D, Treadaway J, Minegishi Y, Rohrer J. Mutations in btk in patients with presumed X-linked agammaglobulinemia. Am J Hum Genet. 1998 May;62(5):1034-43. PMID:9545398 doi:S0002-9297(07)61523-7
  21. ↑ Holinski-Feder E, Weiss M, Brandau O, Jedele KB, Nore B, Backesjo CM, Vihinen M, Hubbard SR, Belohradsky BH, Smith CI, Meindl A. Mutation screening of the BTK gene in 56 families with X-linked agammaglobulinemia (XLA): 47 unique mutations without correlation to clinical course. Pediatrics. 1998 Feb;101(2):276-84. PMID:9445504
  22. ↑ Vihinen M, Kwan SP, Lester T, Ochs HD, Resnick I, Valiaho J, Conley ME, Smith CI. Mutations of the human BTK gene coding for bruton tyrosine kinase in X-linked agammaglobulinemia. Hum Mutat. 1999;13(4):280-5. PMID:10220140 doi:<280::AID-HUMU3>3.0.CO;2-L 10.1002/(SICI)1098-1004(1999)13:4<280::AID-HUMU3>3.0.CO;2-L
  23. ↑ Curtis SK, Hebert MD, Saha BK. Twin carriers of X-linked agammaglobulinemia (XLA) due to germline mutation in the Btk gene. Am J Med Genet. 2000 Jan 31;90(3):229-32. PMID:10678660
  24. ↑ Orlandi P, Ritis K, Moschese V, Angelini F, Arvanitidis K, Speletas M, Sideras P, Plebani A, Rossi P. Identification of nine novel mutations in the Bruton's tyrosine kinase gene in X-linked agammaglobulinaemia patients. Hum Mutat. 2000 Jan;15(1):117. PMID:10612838 doi:<117::AID-HUMU26>3.0.CO;2-H 10.1002/(SICI)1098-1004(200001)15:1<117::AID-HUMU26>3.0.CO;2-H
  25. ↑ Yang W, Desiderio S. BAP-135, a target for Bruton's tyrosine kinase in response to B cell receptor engagement. Proc Natl Acad Sci U S A. 1997 Jan 21;94(2):604-9. PMID:9012831
  26. ↑ Rodriguez R, Matsuda M, Perisic O, Bravo J, Paul A, Jones NP, Light Y, Swann K, Williams RL, Katan M. Tyrosine residues in phospholipase Cgamma 2 essential for the enzyme function in B-cell signaling. J Biol Chem. 2001 Dec 21;276(51):47982-92. Epub 2001 Oct 17. PMID:11606584 doi:10.1074/jbc.M107577200
  27. ↑ Horwood NJ, Page TH, McDaid JP, Palmer CD, Campbell J, Mahon T, Brennan FM, Webster D, Foxwell BM. Bruton's tyrosine kinase is required for TLR2 and TLR4-induced TNF, but not IL-6, production. J Immunol. 2006 Mar 15;176(6):3635-41. PMID:16517732
  28. ↑ Rajaiya J, Nixon JC, Ayers N, Desgranges ZP, Roy AL, Webb CF. Induction of immunoglobulin heavy-chain transcription through the transcription factor Bright requires TFII-I. Mol Cell Biol. 2006 Jun;26(12):4758-68. PMID:16738337 doi:10.1128/MCB.02009-05
  29. ↑ Mansell A, Smith R, Doyle SL, Gray P, Fenner JE, Crack PJ, Nicholson SE, Hilton DJ, O'Neill LA, Hertzog PJ. Suppressor of cytokine signaling 1 negatively regulates Toll-like receptor signaling by mediating Mal degradation. Nat Immunol. 2006 Feb;7(2):148-55. Epub 2006 Jan 15. PMID:16415872 doi:10.1038/ni1299
  30. ↑ Doyle SL, Jefferies CA, Feighery C, O'Neill LA. Signaling by Toll-like receptors 8 and 9 requires Bruton's tyrosine kinase. J Biol Chem. 2007 Dec 21;282(51):36953-60. Epub 2007 Oct 11. PMID:17932028 doi:10.1074/jbc.M707682200
  31. ↑ Damm-Ganamet KL, Arora N, Becart S, Edwards JP, Lebsack AD, McAllister H, Nelen MI, Rao N, Westover L, Wiener JJM, Mirzadegan T. Accelerating Lead Identification by High Throughput Virtual Screening: Prospective Case Studies from the Pharmaceutical Industry. J Chem Inf Model. 2019 Feb 28. doi: 10.1021/acs.jcim.8b00941. PMID:30817167 doi:http://dx.doi.org/10.1021/acs.jcim.8b00941

6nfi, resolution 2.41Å

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