|Entry||Database: PDB / ID: 3ce3|
|Title||Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-MET in complex with a Pyrrolopyridinepyridone based inhibitor|
|Components||Hepatocyte growth factor receptorC-Met|
|Keywords||TRANSFERASE / RECEPTOR TYROSINE KINASE / SIGNAL TRANSDUCTION / GRB2 / SHC / ATP-BINDING / GLYCOPROTEIN / MEMBRANE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / PROTO-ONCOGENE / TRANSMEMBRANE / TYROSINE-PROTEIN KINASE|
|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 / negative regulation of Rho protein signal transduction / MET activates PI3K/AKT signaling / MET activates RAP1 and RAC1 / 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 superfamily / Sema domain profile. / Sema domain / IPT/TIG domain ...Tyrosine-protein kinase, HGF/MSP receptor / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain superfamily / Sema domain profile. / Sema domain / IPT/TIG domain / ig-like, plexins, transcription factors / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin E-set / Tyrosine kinase, catalytic domain / Tyrosine-protein 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinases ATP-binding region signature. / Protein kinase, ATP binding site / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-1FN / Hepatocyte growth factor receptor
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å|
|Citation||Journal: J.Med.Chem. / Year: 2008|
Title: Discovery of pyrrolopyridine-pyridone based inhibitors of Met kinase: synthesis, X-ray crystallographic analysis, and biological activities.
Authors: Kim, K.S. / Zhang, L. / Schmidt, R. / Cai, Z.W. / Wei, D. / Williams, D.K. / Lombardo, L.J. / Trainor, G.L. / Xie, D. / Zhang, Y. / An, Y. / Sack, J.S. / Tokarski, J.S. / Darienzo, C. / ...Authors: Kim, K.S. / Zhang, L. / Schmidt, R. / Cai, Z.W. / Wei, D. / Williams, D.K. / Lombardo, L.J. / Trainor, G.L. / Xie, D. / Zhang, Y. / An, Y. / Sack, J.S. / Tokarski, J.S. / Darienzo, C. / Kamath, A. / Marathe, P. / Zhang, Y. / Lippy, J. / Jeyaseelan, R. / Wautlet, B. / Henley, B. / Gullo-Brown, J. / Manne, V. / Hunt, J.T. / Fargnoli, J. / Borzilleri, R.M.
|Structure viewer||Molecule: |
Downloads & links
A: Hepatocyte growth factor receptor
|#1: Protein|| |
Mass: 35435.031 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN, UNP RESIDUES 1049-1360 / Mutation: Y1194F, Y1234F, Y1235D, V1272L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Cell line (production host): SPODOPTERA FRUGIPERDA 9 (Sf9) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P08581, receptor protein-tyrosine kinase
|#2: Chemical|| ChemComp-1FN / |
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 %|
|Crystal grow||pH: 7.1 |
Details: 12% MEPEG 5000, 0.1M HEPES, 11% 2-PROPANOL., pH 7.1
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1|
|Detector||Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2005|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1 Å / Relative weight: 1|
|Reflection||Resolution: 2.4→50 Å / Num. obs: 10949 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 53.116 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 10|
|Reflection shell||Resolution: 2.4→2.49 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.1 / % possible all: 69.9|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 |
|Displacement parameters||Biso mean: 71.35 Å2|
|Refinement step||Cycle: LAST / Resolution: 2.4→50 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2.4→2.54 Å / Total num. of bins used: 9 |
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