|Entry||Database: PDB / ID: 5hti|
|Title||Crystal structure of c-Met kinase domain in complex with LXM108|
|Components||Hepatocyte growth factor receptorC-Met|
|Keywords||TRANSFERASE / c-Met 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 / 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
Chem-66L / Hepatocyte growth factor receptor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å|
|Authors||Liu, Q.F. / Xu, Y.C.|
|Citation||Journal: to be published|
Title: Crystal structure of c-Met kinase domain in complex with LXM108
Authors: Xu, Y.C. / Long, Y.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor receptor
|#1: Protein|| |
Mass: 36033.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P08581, receptor protein-tyrosine kinase
|#2: Chemical|| ChemComp-66L / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.19 Å3/Da / Density % sol: 43.9 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 |
Details: 10-11% PEG5000MME, 11% isopropanol, 0.1M HEPES pH 7.1
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å|
|Detector||Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2015|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Reflection||Resolution: 1.66→50 Å / Num. obs: 38131 / % possible obs: 99.7 % / Redundancy: 10.8 % / Biso Wilson estimate: 17.12 Å2 / Rmerge(I) obs: 0.072 / Net I/av σ(I): 38.262 / Net I/σ(I): 7.8|
|Phasing||Method: molecular replacement|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4MXC
Resolution: 1.66→31.283 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.44
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Displacement parameters||Biso max: 66.54 Å2 / Biso mean: 23.6161 Å2 / Biso min: 7.94 Å2|
|Refinement step||Cycle: final / Resolution: 1.66→31.283 Å|
|Refine LS restraints|
|LS refinement shell|
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