8beb: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8beb]] 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=8BEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BEB FirstGlance]. <br>
<table><tr><td colspan='2'>[[8beb]] 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=8BEB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BEB FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QIK:(2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]butylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide'>QIK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.18&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=QIK:(2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]butylamino]-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-3-oxidanylidene-propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide'>QIK</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=8beb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8beb OCA], [https://pdbe.org/8beb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8beb RCSB], [https://www.ebi.ac.uk/pdbsum/8beb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8beb ProSAT]</span></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=8beb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8beb OCA], [https://pdbe.org/8beb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8beb RCSB], [https://www.ebi.ac.uk/pdbsum/8beb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8beb ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
== Function ==
[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.<ref>PMID:9751722</ref> <ref>PMID:10944113</ref> <ref>PMID:19584355</ref>  
[https://www.uniprot.org/uniprot/VHL_HUMAN VHL_HUMAN] Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.<ref>PMID:9751722</ref> <ref>PMID:10944113</ref> <ref>PMID:19584355</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Herein, we describe a systematic SAR- and SPR-investigation of the peptidomimetic hydroxy-proline based VHL-ligand VH032, from which most to-date published VHL-targeting PROTACs have been derived. This study provides for the first time a consistent data set which allows for direct comparison of structural variations including those which were so far hidden in patent literature. The gained knowledge about improved VHL binders was used to design a small library of highly potent BRD4-degraders comprising different VHL exit vectors. Newly designed degraders showed favorable molecular properties and significantly improved degradation potency compared to MZ1.
Systematic Potency &amp; Property Assessment of VHL Ligands and Implications on PROTAC Design.,Krieger J, Sorell FJ, Wegener AA, Leuthner B, Machrouhi-Porcher F, Hecht M, Leibrock EM, Mueller JE, Eisert J, Hartung IV, Schlesiger S ChemMedChem. 2023 Feb 7. doi: 10.1002/cmdc.202200615. PMID:36749883<ref>PMID:36749883</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8beb" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 11:17, 7 February 2024

Ternary complex between VCB, BRD4-BD1 and PROTAC 49Ternary complex between VCB, BRD4-BD1 and PROTAC 49

Structural highlights

8beb 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 3.18Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

VHL_HUMAN Defects in VHL are a cause of susceptibility to pheochromocytoma (PCC) [MIM:171300. A catecholamine-producing tumor of chromaffin tissue of the adrenal medulla or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of epinephrine and norepinephrine, is hypertension, which may be persistent or intermittent. Defects in VHL are the cause of von Hippel-Lindau disease (VHLD) [MIM:193300. VHLD is a dominantly inherited familial cancer syndrome characterized by the development of retinal angiomatosis, cerebellar and spinal hemangioblastoma, renal cell carcinoma (RCC), phaeochromocytoma and pancreatic tumors. VHL type 1 is without pheochromocytoma, type 2 is with pheochromocytoma. VHL type 2 is further subdivided into types 2A (pheochromocytoma, retinal angioma, and hemangioblastomas without renal cell carcinoma and pancreatic cyst) and 2B (pheochromocytoma, retinal angioma, and hemangioblastomas with renal cell carcinoma and pancreatic cyst). VHL type 2C refers to patients with isolated pheochromocytoma without hemangioblastoma or renal cell carcinoma. The estimated incidence is 3/100000 births per year and penetrance is 97% by age 60 years.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [:][15] [16] [17] Defects in VHL are the cause of familial erythrocytosis type 2 (ECYT2) [MIM:263400; also called VHL-dependent polycythemia or Chuvash type polycythemia. ECYT2 is an autosomal recessive disorder characterized by an increase in serum red blood cell mass, hypersensitivity of erythroid progenitors to erythropoietin, increased erythropoietin serum levels, and normal oxygen affinity. Patients with ECYT2 carry a high risk for peripheral thrombosis and cerebrovascular events.[18] [19] Defects in VHL are a cause of renal cell carcinoma (RCC) [MIM:144700. Renal cell carcinoma is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.[20]

Function

VHL_HUMAN Involved in the ubiquitination and subsequent proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Seems to act as target recruitment subunit in the E3 ubiquitin ligase complex and recruits hydroxylated hypoxia-inducible factor (HIF) under normoxic conditions. Involved in transcriptional repression through interaction with HIF1A, HIF1AN and histone deacetylases. Ubiquitinates, in an oxygen-responsive manner, ADRB2.[21] [22] [23]

References

  1. ↑ Feldman DE, Thulasiraman V, Ferreyra RG, Frydman J. Formation of the VHL-elongin BC tumor suppressor complex is mediated by the chaperonin TRiC. Mol Cell. 1999 Dec;4(6):1051-61. PMID:10635329
  2. ↑ Latif F, Tory K, Gnarra J, Yao M, Duh FM, Orcutt ML, Stackhouse T, Kuzmin I, Modi W, Geil L, et al.. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science. 1993 May 28;260(5112):1317-20. PMID:8493574
  3. ↑ Crossey PA, Richards FM, Foster K, Green JS, Prowse A, Latif F, Lerman MI, Zbar B, Affara NA, Ferguson-Smith MA, et al.. Identification of intragenic mutations in the von Hippel-Lindau disease tumour suppressor gene and correlation with disease phenotype. Hum Mol Genet. 1994 Aug;3(8):1303-8. PMID:7987306
  4. ↑ Chen F, Kishida T, Yao M, Hustad T, Glavac D, Dean M, Gnarra JR, Orcutt ML, Duh FM, Glenn G, et al.. Germline mutations in the von Hippel-Lindau disease tumor suppressor gene: correlations with phenotype. Hum Mutat. 1995;5(1):66-75. PMID:7728151 doi:http://dx.doi.org/10.1002/humu.1380050109
  5. ↑ . Germline mutations in the von Hippel-Lindau disease (VHL) gene in Japanese VHL. Clinical Research Group for VHL in Japan. Hum Mol Genet. 1995 Dec;4(12):2233-7. PMID:8634692
  6. ↑ Crossey PA, Eng C, Ginalska-Malinowska M, Lennard TW, Wheeler DC, Ponder BA, Maher ER. Molecular genetic diagnosis of von Hippel-Lindau disease in familial phaeochromocytoma. J Med Genet. 1995 Nov;32(11):885-6. PMID:8592333
  7. ↑ Eng C, Crossey PA, Mulligan LM, Healey CS, Houghton C, Prowse A, Chew SL, Dahia PL, O'Riordan JL, Toledo SP, et al.. Mutations in the RET proto-oncogene and the von Hippel-Lindau disease tumour suppressor gene in sporadic and syndromic phaeochromocytomas. J Med Genet. 1995 Dec;32(12):934-7. PMID:8825918
  8. ↑ Maher ER, Webster AR, Richards FM, Green JS, Crossey PA, Payne SJ, Moore AT. Phenotypic expression in von Hippel-Lindau disease: correlations with germline VHL gene mutations. J Med Genet. 1996 Apr;33(4):328-32. PMID:8730290
  9. ↑ Zbar B, Kishida T, Chen F, Schmidt L, Maher ER, Richards FM, Crossey PA, Webster AR, Affara NA, Ferguson-Smith MA, Brauch H, Glavac D, Neumann HP, Tisherman S, Mulvihill JJ, Gross DJ, Shuin T, Whaley J, Seizinger B, Kley N, Olschwang S, Boisson C, Richard S, Lips CH, Lerman M, et al.. Germline mutations in the Von Hippel-Lindau disease (VHL) gene in families from North America, Europe, and Japan. Hum Mutat. 1996;8(4):348-57. PMID:8956040 doi:<348::AID-HUMU8>3.0.CO;2-3 10.1002/(SICI)1098-1004(1996)8:4<348::AID-HUMU8>3.0.CO;2-3
  10. ↑ Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerstrom G, Nordenskjold M, Bergerheim US. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Hum Mutat. 1998;Suppl 1:S31-3. PMID:9452032
  11. ↑ Mandich P, Montera M, Bellone E, Trojani A, Daniele S, Ajmar F. Three novel mutations in the Von Hippel-Lindau tumour suppressor gene in Italian patients. Hum Mutat. 1998;Suppl 1:S268-70. PMID:9452106
  12. ↑ Martin R, Hockey A, Walpole I, Goldblatt J. Variable penetrance of familial pheochromocytoma associated with the von Hipple Lindau gene mutation, S68W. Mutations in brief no. 150. Online. Hum Mutat. 1998;12(1):71. PMID:10627136 doi:<71::AID-HUMU14>3.0.CO;2-A 10.1002/(SICI)1098-1004(1998)12:1<71::AID-HUMU14>3.0.CO;2-A
  13. ↑ Stolle C, Glenn G, Zbar B, Humphrey JS, Choyke P, Walther M, Pack S, Hurley K, Andrey C, Klausner R, Linehan WM. Improved detection of germline mutations in the von Hippel-Lindau disease tumor suppressor gene. Hum Mutat. 1998;12(6):417-23. PMID:9829911 doi:<417::AID-HUMU8>3.0.CO;2-K 10.1002/(SICI)1098-1004(1998)12:6<417::AID-HUMU8>3.0.CO;2-K
  14. ↑ Olschwang S, Richard S, Boisson C, Giraud S, Laurent-Puig P, Resche F, Thomas G. Germline mutation profile of the VHL gene in von Hippel-Lindau disease and in sporadic hemangioblastoma. Hum Mutat. 1998;12(6):424-30. PMID:9829912 doi:<424::AID-HUMU9>3.0.CO;2-H 10.1002/(SICI)1098-1004(1998)12:6<424::AID-HUMU9>3.0.CO;2-H
  15. ↑ Bradley JF, Collins DL, Schimke RN, Parrott HN, Rothberg PG. Two distinct phenotypes caused by two different missense mutations in the same codon of the VHL gene. Am J Med Genet. 1999 Nov 19;87(2):163-7. PMID:10533030
  16. ↑ Gallou C, Joly D, Mejean A, Staroz F, Martin N, Tarlet G, Orfanelli MT, Bouvier R, Droz D, Chretien Y, Marechal JM, Richard S, Junien C, Beroud C. Mutations of the VHL gene in sporadic renal cell carcinoma: definition of a risk factor for VHL patients to develop an RCC. Hum Mutat. 1999;13(6):464-75. PMID:10408776 doi:<464::AID-HUMU6>3.0.CO;2-A 10.1002/(SICI)1098-1004(1999)13:6<464::AID-HUMU6>3.0.CO;2-A
  17. ↑ Abbott MA, Nathanson KL, Nightingale S, Maher ER, Greenstein RM. The von Hippel-Lindau (VHL) germline mutation V84L manifests as early-onset bilateral pheochromocytoma. Am J Med Genet A. 2006 Apr 1;140(7):685-90. PMID:16502427 doi:10.1002/ajmg.a.31116
  18. ↑ Pastore Y, Jedlickova K, Guan Y, Liu E, Fahner J, Hasle H, Prchal JF, Prchal JT. Mutations of von Hippel-Lindau tumor-suppressor gene and congenital polycythemia. Am J Hum Genet. 2003 Aug;73(2):412-9. Epub 2003 Jul 3. PMID:12844285 doi:S0002-9297(07)61930-2
  19. ↑ Pastore YD, Jelinek J, Ang S, Guan Y, Liu E, Jedlickova K, Krishnamurti L, Prchal JT. Mutations in the VHL gene in sporadic apparently congenital polycythemia. Blood. 2003 Feb 15;101(4):1591-5. Epub 2002 Oct 10. PMID:12393546 doi:10.1182/blood-2002-06-1843
  20. ↑ Wiesener MS, Seyfarth M, Warnecke C, Jurgensen JS, Rosenberger C, Morgan NV, Maher ER, Frei U, Eckardt KU. Paraneoplastic erythrocytosis associated with an inactivating point mutation of the von Hippel-Lindau gene in a renal cell carcinoma. Blood. 2002 May 15;99(10):3562-5. PMID:11986208
  21. ↑ Iliopoulos O, Ohh M, Kaelin WG Jr. pVHL19 is a biologically active product of the von Hippel-Lindau gene arising from internal translation initiation. Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11661-6. PMID:9751722
  22. ↑ Tanimoto K, Makino Y, Pereira T, Poellinger L. Mechanism of regulation of the hypoxia-inducible factor-1 alpha by the von Hippel-Lindau tumor suppressor protein. EMBO J. 2000 Aug 15;19(16):4298-309. PMID:10944113 doi:10.1093/emboj/19.16.4298
  23. ↑ Xie L, Xiao K, Whalen EJ, Forrester MT, Freeman RS, Fong G, Gygi SP, Lefkowitz RJ, Stamler JS. Oxygen-regulated beta(2)-adrenergic receptor hydroxylation by EGLN3 and ubiquitylation by pVHL. Sci Signal. 2009 Jul 7;2(78):ra33. doi: 10.1126/scisignal.2000444. PMID:19584355 doi:10.1126/scisignal.2000444

8beb, resolution 3.18Å

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