|Entry||Database: PDB / ID: 7b3v|
|Title||Crystal structure of c-MET bound by compound 3|
|Components||Hepatocyte growth factor receptorC-Met|
|Keywords||TRANSFERASE / c-met / kinase / folded P-loop / 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 / MET activates PTPN11 / pancreas development / MET activates RAP1 and RAC1 / MET activates PI3K/AKT signaling / negative regulation of Rho protein signal transduction / negative regulation of stress fiber assembly / semaphorin-plexin signaling pathway / MET activates PTK2 signaling / negative regulation of thrombin-activated receptor signaling pathway / branching morphogenesis of an epithelial tube / positive chemotaxis / establishment of skin barrier / MET activates RAS signaling / MECP2 regulates neuronal receptors and channels / phagocytosis / positive regulation of microtubule polymerization / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / neuron differentiation / Negative regulation of MET activity / 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 phosphatase binding / protein tyrosine kinase activity / positive regulation of protein kinase B signaling / cell surface receptor signaling pathway / receptor complex / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / 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 superfamily / Sema domain profile. / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / 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 / 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
Similarity search - Domain/homology
Chem-SWB / Hepatocyte growth factor receptor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å|
|Citation||Journal: Acs Med.Chem.Lett. / Year: 2021|
Title: Structural Basis for Targeting the Folded P-Loop Conformation of c-MET.
Authors: Collie, G.W. / Michaelides, I.N. / Embrey, K. / Stubbs, C.J. / Borjesson, U. / Dale, I.L. / Snijder, A. / Barlind, L. / Song, K. / Khurana, P. / Phillips, C. / Storer, R.I.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor receptor
|#1: Protein|| |
Mass: 33786.207 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-SWB / |
|#3: Water|| ChemComp-HOH / |
|Has ligand of interest||Y|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.6 Å3/Da / Density % sol: 52.73 %|
|Crystal grow||Temperature: 273 K / Method: vapor diffusion, sitting drop / Details: 25 % PEG3350, 0.2 M (NH4)2SO4, PCPT pH 5.5|
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å|
|Detector||Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 1, 2017|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97625 Å / Relative weight: 1|
|Reflection||Resolution: 1.93→28.71 Å / Num. obs: 26013 / % possible obs: 98 % / Redundancy: 3.2 % / CC1/2: 0.993 / Net I/σ(I): 18.8|
|Reflection shell||Resolution: 1.93→1.96 Å / Num. unique obs: 1206 / CC1/2: 0.936|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: internal
Resolution: 1.93→22.61 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.897 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.147
|Displacement parameters||Biso max: 88.5 Å2 / Biso mean: 28.99 Å2 / Biso min: 11.28 Å2|
|Refine analyze||Luzzati coordinate error obs: 0.32 Å|
|Refinement step||Cycle: final / Resolution: 1.93→22.61 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 1.93→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13 |
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