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2xyu

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Revision as of 12:26, 22 July 2020

Crystal structure of EphA4 kinase domain in complex with VUF 12058

Structural highlights

2xyu is a 1 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1b0x
Activity:	Receptor protein-tyrosine kinase, with EC number 2.7.10.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[EPHA4_MOUSE] Receptor tyrosine kinase which binds membrane-bound ephrin family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Highly promiscuous, it has the unique property among Eph receptors to bind and to be physiologically activated by both GPI-anchored ephrin-A and transmembrane ephrin-B ligands including EFNA1 and EFNB3. Upon activation by ephrin ligands, modulates cell morphology and integrin-dependent cell adhesion through regulation of the Rac, Rap and Rho GTPases activity. Plays an important role in the development of the nervous system controlling different steps of axonal guidance including the establishment of the corticospinal projections. May also control the segregation of motor and sensory axons during neuromuscular circuit development. Beside its role in axonal guidance plays a role in synaptic plasticity. Activated by EFNA1 phosphorylates CDK5 at 'Tyr-15' which in turn phosphorylates NGEF regulating RHOA and dendritic spine morphogenesis. In the nervous system, plays also a role in repair after injury preventing axonal regeneration and in angiogenesis playing a role in central nervous system vascular formation. Additionally, its promiscuity makes it available to participate in a variety of cell-cell signaling regulating for instance the development of the thymic epithelium.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in silico screening procedure which was focused on finding novel, EPHA4 hinge binding fragments. This resulted in the identification of 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine derivatives as EPHA4 inhibitors. Hit exploration yielded a compound with 2 muM (IC(50)) affinity for the EPHA4 receptor tyrosine kinase domain. Soaking experiments into a crystal of the EPHA4 kinase domain gave a 2.11A X-ray structure of the EPHA4 - inhibitor complex, which confirmed the binding mode of the scaffold as proposed by the initial in silico work. The results underscore the strength of fragment based in silico screening as a tool for the discovery of novel lead compounds as small molecule kinase inhibitors.

Fragment based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase.,van Linden OP, Farenc C, Zoutman WH, Hameetman L, Wijtmans M, Leurs R, Tensen CP, Siegal G, de Esch IJ Eur J Med Chem. 2011 Nov 18. PMID:22137457^[10]

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

References

↑ Dottori M, Hartley L, Galea M, Paxinos G, Polizzotto M, Kilpatrick T, Bartlett PF, Murphy M, Kontgen F, Boyd AW. EphA4 (Sek1) receptor tyrosine kinase is required for the development of the corticospinal tract. Proc Natl Acad Sci U S A. 1998 Oct 27;95(22):13248-53. PMID:9789074
↑ Goldshmit Y, Galea MP, Wise G, Bartlett PF, Turnley AM. Axonal regeneration and lack of astrocytic gliosis in EphA4-deficient mice. J Neurosci. 2004 Nov 10;24(45):10064-73. PMID:15537875 doi:http://dx.doi.org/10.1523/JNEUROSCI.2981-04.2004
↑ Goldshmit Y, Galea MP, Bartlett PF, Turnley AM. EphA4 regulates central nervous system vascular formation. J Comp Neurol. 2006 Aug 20;497(6):864-75. PMID:16802330 doi:http://dx.doi.org/10.1002/cne.21029
↑ Munoz JJ, Alfaro D, Garcia-Ceca J, Alonso-C LM, Jimenez E, Zapata A. Thymic alterations in EphA4-deficient mice. J Immunol. 2006 Jul 15;177(2):804-13. PMID:16818734
↑ Iwasato T, Katoh H, Nishimaru H, Ishikawa Y, Inoue H, Saito YM, Ando R, Iwama M, Takahashi R, Negishi M, Itohara S. Rac-GAP alpha-chimerin regulates motor-circuit formation as a key mediator of EphrinB3/EphA4 forward signaling. Cell. 2007 Aug 24;130(4):742-53. PMID:17719550 doi:http://dx.doi.org/10.1016/j.cell.2007.07.022
↑ Richter M, Murai KK, Bourgin C, Pak DT, Pasquale EB. The EphA4 receptor regulates neuronal morphology through SPAR-mediated inactivation of Rap GTPases. J Neurosci. 2007 Dec 19;27(51):14205-15. PMID:18094260 doi:http://dx.doi.org/10.1523/JNEUROSCI.2746-07.2007
↑ Fu WY, Chen Y, Sahin M, Zhao XS, Shi L, Bikoff JB, Lai KO, Yung WH, Fu AK, Greenberg ME, Ip NY. Cdk5 regulates EphA4-mediated dendritic spine retraction through an ephexin1-dependent mechanism. Nat Neurosci. 2007 Jan;10(1):67-76. Epub 2006 Dec 3. PMID:17143272 doi:10.1038/nn1811
↑ Beg AA, Sommer JE, Martin JH, Scheiffele P. alpha2-Chimaerin is an essential EphA4 effector in the assembly of neuronal locomotor circuits. Neuron. 2007 Sep 6;55(5):768-78. PMID:17785183 doi:http://dx.doi.org/10.1016/j.neuron.2007.07.036
↑ Gallarda BW, Bonanomi D, Muller D, Brown A, Alaynick WA, Andrews SE, Lemke G, Pfaff SL, Marquardt T. Segregation of axial motor and sensory pathways via heterotypic trans-axonal signaling. Science. 2008 Apr 11;320(5873):233-6. doi: 10.1126/science.1153758. PMID:18403711 doi:http://dx.doi.org/10.1126/science.1153758
↑ van Linden OP, Farenc C, Zoutman WH, Hameetman L, Wijtmans M, Leurs R, Tensen CP, Siegal G, de Esch IJ. Fragment based lead discovery of small molecule inhibitors for the EPHA4 receptor tyrosine kinase. Eur J Med Chem. 2011 Nov 18. PMID:22137457 doi:10.1016/j.ejmech.2011.11.020

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/2xyu"

@@ Line 1: / Line 1: @@
 ==Crystal structure of EphA4 kinase domain in complex with VUF 12058==
-<StructureSection load='2xyu' size='340' side='right' caption='[[2xyu]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
+<StructureSection load='2xyu' size='340' side='right'caption='[[2xyu]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XYU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xyu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XYU OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XYU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=Q9G:5-(5-FLUORO-2-METHYLPHENYL)-6,7,8,9-TETRAHYDRO-3H-PYRAZOLO[3,4-C]ISOQUINOLIN-1-AMINE'>Q9G</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=Q9G:5-(5-FLUORO-2-METHYLPHENYL)-6,7,8,9-TETRAHYDRO-3H-PYRAZOLO[3,4-C]ISOQUINOLIN-1-AMINE'>Q9G</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1b0x|1b0x]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Receptor_protein-tyrosine_kinase Receptor protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.1 2.7.10.1] </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=2xyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyu OCA], [http://pdbe.org/2xyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xyu RCSB], [http://www.ebi.ac.uk/pdbsum/2xyu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyu ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2xyu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xyu OCA], [http://pdbe.org/2xyu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xyu RCSB], [http://www.ebi.ac.uk/pdbsum/2xyu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xyu ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 22: / Line 22: @@
 ==See Also==
-*[[Ephrin receptor|Ephrin receptor]]
+*[[Ephrin receptor 3D structures|Ephrin receptor 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Lk3 transgenic mice]]
 [[Category: Receptor protein-tyrosine kinase]]

2xyu

From Proteopedia

Revision as of 12:26, 22 July 2020

Crystal structure of EphA4 kinase domain in complex with VUF 12058

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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