|Entry||Database: PDB / ID: 6sde|
|Title||Crystal structure of wild-type cMET bound by savolitinib|
|Components||Hepatocyte growth factor receptorC-Met|
|Keywords||TRANSFERASE / Kinase / inhibitor|
|Function / homology|
Function and homology information
hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity ...hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / MET activates STAT3 / endothelial cell morphogenesis / negative regulation of hydrogen peroxide-mediated programmed cell death / negative regulation of guanyl-nucleotide exchange factor activity / MET interacts with TNS proteins / MET Receptor Activation / positive regulation of endothelial cell chemotaxis / semaphorin receptor activity / MET receptor recycling / Sema4D mediated inhibition of cell attachment and migration / pancreas development / MET activates PTPN11 / negative regulation of Rho protein signal transduction / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / establishment of skin barrier / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / MET activates RAS signaling / phagocytosis / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / Negative regulation of MET activity / neuron differentiation / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / positive regulation of kinase activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / transmembrane receptor protein tyrosine kinase signaling pathway / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / positive regulation of protein kinase B signaling / protein phosphatase binding / cell surface receptor signaling pathway / receptor complex / cell surface / signal transduction / plasma membrane => GO:0005886 / positive regulation of transcription by RNA polymerase II / extracellular region / membrane => GO:0016020 / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain profile. / Sema domain superfamily / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain profile. / Sema domain superfamily / IPT/TIG domain / ig-like, plexins, transcription factors / domain found in Plexins, Semaphorins and Integrins / PSI domain / IPT domain / Immunoglobulin E-set / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
volitinib / Hepatocyte growth factor receptor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å|
|Authors||Collie, G.W. / Phillips, C.|
|Citation||Journal: Acs Med.Chem.Lett. / Year: 2019|
Title: Structural and Molecular Insight into Resistance Mechanisms of First Generation cMET Inhibitors.
Authors: Collie, G.W. / Koh, C.M. / O'Neill, D.J. / Stubbs, C.J. / Khurana, P. / Eddershaw, A. / Snijder, A. / Mauritzson, F. / Barlind, L. / Dale, I.L. / Shaw, J. / Phillips, C. / Hennessy, E.J. / ...Authors: Collie, G.W. / Koh, C.M. / O'Neill, D.J. / Stubbs, C.J. / Khurana, P. / Eddershaw, A. / Snijder, A. / Mauritzson, F. / Barlind, L. / Dale, I.L. / Shaw, J. / Phillips, C. / Hennessy, E.J. / Cheung, T. / Narvaez, A.J.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor receptor
|#1: Protein|| |
Mass: 34842.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Escherichia coli (E. coli)
References: UniProt: P08581, receptor protein-tyrosine kinase
|#2: Chemical|| ChemComp-V0L / |
|#3: Water|| ChemComp-HOH / |
|Has ligand of interest||Y|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.34 Å3/Da / Density % sol: 47.34 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15 % 2-propanol, 15 % PEG4K, 0.2 M PCPT pH 7.5|
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98003 Å|
|Detector||Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2017|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.98003 Å / Relative weight: 1|
|Reflection||Resolution: 2.49→43.36 Å / Num. obs: 10493 / % possible obs: 99.1 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 8.8|
|Reflection shell||Resolution: 2.49→2.56 Å / Num. unique obs: 718 / CC1/2: 0.427|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 2WGJ
Resolution: 2.49→41.78 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.849 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.598 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.721 / SU Rfree Blow DPI: 0.317 / SU Rfree Cruickshank DPI: 0.314
|Displacement parameters||Biso max: 161 Å2 / Biso mean: 69.55 Å2 / Biso min: 34.86 Å2|
|Refine analyze||Luzzati coordinate error obs: 0.3 Å|
|Refinement step||Cycle: final / Resolution: 2.49→41.78 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.49→2.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5 |
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
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