6st3: Difference between revisions

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'''Unreleased structure'''


The entry 6st3 is ON HOLD
==HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide==
<StructureSection load='6st3' size='340' side='right'caption='[[6st3]], [[Resolution|resolution]] 2.43&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6st3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ST3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ST3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=LUW:4-oxidanyl-~{N}-[(4-phenoxyphenyl)methyl]-2-pyrazol-1-yl-pyrimidine-5-carboxamide'>LUW</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Hypoxia-inducible_factor-proline_dioxygenase Hypoxia-inducible factor-proline dioxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.11.29 1.14.11.29] </span></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=6st3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6st3 OCA], [http://pdbe.org/6st3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6st3 RCSB], [http://www.ebi.ac.uk/pdbsum/6st3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6st3 ProSAT]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/EGLN1_HUMAN EGLN1_HUMAN]] Defects in EGLN1 are the cause of familial erythrocytosis type 3 (ECYT3) [MIM:[http://omim.org/entry/609820 609820]]. ECYT3 is an autosomal dominant disorder characterized by increased serum red blood cell mass, elevated serum hemoglobin and hematocrit, and normal serum erythropoietin levels.<ref>PMID:16407130</ref> <ref>PMID:17579185</ref> 
== Function ==
[[http://www.uniprot.org/uniprot/EGLN1_HUMAN EGLN1_HUMAN]] Cellular oxygen sensor that catalyzes, under normoxic conditions, the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates a specific proline found in each of the oxygen-dependent degradation (ODD) domains (N-terminal, NODD, and C-terminal, CODD) of HIF1A. Also hydroxylates HIF2A. Has a preference for the CODD site for both HIF1A and HIF1B. Hydroxylated HIFs are then targeted for proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is attenuated allowing HIFs to escape degradation resulting in their translocation to the nucleus, heterodimerization with HIF1B, and increased expression of hypoxy-inducible genes. EGLN1 is the most important isozyme under normoxia and, through regulating the stability of HIF1, involved in various hypoxia-influenced processes such as angiogenesis in retinal and cardiac functionality.<ref>PMID:11595184</ref> <ref>PMID:12351678</ref> <ref>PMID:15897452</ref> <ref>PMID:19339211</ref> <ref>PMID:21792862</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 2-oxoglutarate-dependent hypoxia inducible factor prolyl hydroxylases (PHDs) are targets for treatment of a variety of disease states including anemia. One PHD inhibitor is approved for use in the treatment of renal anemia and others are in late stage clinical trials. However, the number of reported templates for PHD inhibition is limited. We report structure-activity relationship and crystallographic studies on a promising class of 4-hydroxypyrimidine-containing PHD inhibitors.


Authors: Chowdhury, R., Holt-Martyn, J.P., Schofield, C.J.
Structure-Activity Relationship and Crystallographic Studies On 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors.,Holt-Martyn J, Chowdhury R, Tumber A, Yeh TL, Abboud MI, Lippl K, Lohans C, Langley G, McDonough M, Pugh C, Ratcliffe P, Schofield C ChemMedChem. 2019 Nov 21. doi: 10.1002/cmdc.201900557. PMID:31751494<ref>PMID:31751494</ref>


Description: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Holt-Martyn, J.P]]
<div class="pdbe-citations 6st3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Hypoxia-inducible factor-proline dioxygenase]]
[[Category: Large Structures]]
[[Category: Chowdhury, R]]
[[Category: Chowdhury, R]]
[[Category: Schofield, C.J]]
[[Category: Holt-Martyn, J P]]
[[Category: Schofield, C J]]
[[Category: 2-oxoglutarate]]
[[Category: Beta-hydroxylation]]
[[Category: Breast cancer]]
[[Category: Cell structure]]
[[Category: Cytoplasm]]
[[Category: Development]]
[[Category: Dna-binding]]
[[Category: Dsbh]]
[[Category: Egln1]]
[[Category: Facial triad]]
[[Category: Familial erythrocytosis]]
[[Category: Helix-loop-helix-beta]]
[[Category: Hif]]
[[Category: Hif prolyl hydroxylase domain 2]]
[[Category: Hypoxia]]
[[Category: Hypoxia-inducible factor]]
[[Category: Iron]]
[[Category: Metal-binding]]
[[Category: Non-heme dioxygenase]]
[[Category: Oxidoreductase]]
[[Category: Oxygenase]]
[[Category: Phd2]]
[[Category: Polymorphism]]
[[Category: Signaling]]
[[Category: Transcription]]
[[Category: Transcription activator/inhibitor]]
[[Category: Transcription complex]]
[[Category: Transcription/epigenetic regulation]]
[[Category: Ubl conjugation]]
[[Category: Vitamin c]]
[[Category: Zinc-finger]]

Revision as of 11:16, 4 December 2019

HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamideHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with 4-hydroxy-N-(4-phenoxybenzyl)-2-(1H-pyrazol-1-yl)pyrimidine-5-carboxamide

Structural highlights

6st3 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, ,
Activity:Hypoxia-inducible factor-proline dioxygenase, with EC number 1.14.11.29
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[EGLN1_HUMAN] Defects in EGLN1 are the cause of familial erythrocytosis type 3 (ECYT3) [MIM:609820]. ECYT3 is an autosomal dominant disorder characterized by increased serum red blood cell mass, elevated serum hemoglobin and hematocrit, and normal serum erythropoietin levels.[1] [2]

Function

[EGLN1_HUMAN] Cellular oxygen sensor that catalyzes, under normoxic conditions, the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates a specific proline found in each of the oxygen-dependent degradation (ODD) domains (N-terminal, NODD, and C-terminal, CODD) of HIF1A. Also hydroxylates HIF2A. Has a preference for the CODD site for both HIF1A and HIF1B. Hydroxylated HIFs are then targeted for proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is attenuated allowing HIFs to escape degradation resulting in their translocation to the nucleus, heterodimerization with HIF1B, and increased expression of hypoxy-inducible genes. EGLN1 is the most important isozyme under normoxia and, through regulating the stability of HIF1, involved in various hypoxia-influenced processes such as angiogenesis in retinal and cardiac functionality.[3] [4] [5] [6] [7]

Publication Abstract from PubMed

The 2-oxoglutarate-dependent hypoxia inducible factor prolyl hydroxylases (PHDs) are targets for treatment of a variety of disease states including anemia. One PHD inhibitor is approved for use in the treatment of renal anemia and others are in late stage clinical trials. However, the number of reported templates for PHD inhibition is limited. We report structure-activity relationship and crystallographic studies on a promising class of 4-hydroxypyrimidine-containing PHD inhibitors.

Structure-Activity Relationship and Crystallographic Studies On 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors.,Holt-Martyn J, Chowdhury R, Tumber A, Yeh TL, Abboud MI, Lippl K, Lohans C, Langley G, McDonough M, Pugh C, Ratcliffe P, Schofield C ChemMedChem. 2019 Nov 21. doi: 10.1002/cmdc.201900557. PMID:31751494[8]

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

References

  1. ↑ Percy MJ, Zhao Q, Flores A, Harrison C, Lappin TR, Maxwell PH, McMullin MF, Lee FS. A family with erythrocytosis establishes a role for prolyl hydroxylase domain protein 2 in oxygen homeostasis. Proc Natl Acad Sci U S A. 2006 Jan 17;103(3):654-9. Epub 2006 Jan 9. PMID:16407130 doi:0508423103
  2. ↑ Percy MJ, Furlow PW, Beer PA, Lappin TR, McMullin MF, Lee FS. A novel erythrocytosis-associated PHD2 mutation suggests the location of a HIF binding groove. Blood. 2007 Sep 15;110(6):2193-6. Epub 2007 Jun 19. PMID:17579185 doi:10.1182/blood-2007-04-084434
  3. ↑ Epstein AC, Gleadle JM, McNeill LA, Hewitson KS, O'Rourke J, Mole DR, Mukherji M, Metzen E, Wilson MI, Dhanda A, Tian YM, Masson N, Hamilton DL, Jaakkola P, Barstead R, Hodgkin J, Maxwell PH, Pugh CW, Schofield CJ, Ratcliffe PJ. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell. 2001 Oct 5;107(1):43-54. PMID:11595184
  4. ↑ Ivan M, Haberberger T, Gervasi DC, Michelson KS, Gunzler V, Kondo K, Yang H, Sorokina I, Conaway RC, Conaway JW, Kaelin WG Jr. Biochemical purification and pharmacological inhibition of a mammalian prolyl hydroxylase acting on hypoxia-inducible factor. Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13459-64. Epub 2002 Sep 26. PMID:12351678 doi:10.1073/pnas.192342099
  5. ↑ Ozer A, Wu LC, Bruick RK. The candidate tumor suppressor ING4 represses activation of the hypoxia inducible factor (HIF). Proc Natl Acad Sci U S A. 2005 May 24;102(21):7481-6. Epub 2005 May 16. PMID:15897452 doi:0502716102
  6. ↑ Yasumoto K, Kowata Y, Yoshida A, Torii S, Sogawa K. Role of the intracellular localization of HIF-prolyl hydroxylases. Biochim Biophys Acta. 2009 May;1793(5):792-7. doi: 10.1016/j.bbamcr.2009.01.014. , Epub 2009 Feb 5. PMID:19339211 doi:10.1016/j.bbamcr.2009.01.014
  7. ↑ Su Y, Loos M, Giese N, Metzen E, Buchler MW, Friess H, Kornberg A, Buchler P. Prolyl hydroxylase-2 (PHD2) exerts tumor-suppressive activity in pancreatic cancer. Cancer. 2012 Feb 15;118(4):960-72. doi: 10.1002/cncr.26344. Epub 2011 Jul 26. PMID:21792862 doi:10.1002/cncr.26344
  8. ↑ Holt-Martyn J, Chowdhury R, Tumber A, Yeh TL, Abboud MI, Lippl K, Lohans C, Langley G, McDonough M, Pugh C, Ratcliffe P, Schofield C. Structure-Activity Relationship and Crystallographic Studies On 4-Hydroxypyrimidine HIF Prolyl Hydroxylase Domain Inhibitors. ChemMedChem. 2019 Nov 21. doi: 10.1002/cmdc.201900557. PMID:31751494 doi:http://dx.doi.org/10.1002/cmdc.201900557

6st3, resolution 2.43Å

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