+Open data
-Basic information
Entry | Database: PDB / ID: 3cd8 | ||||||
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Title | X-ray Structure of c-Met with triazolopyridazine Inhibitor. | ||||||
Components | Hepatocyte growth factor receptor | ||||||
Keywords | TRANSFERASE / c-Met / Kinase / Triazolopyridazine / ATP-binding / Glycoprotein / Membrane / Nucleotide-binding / Phosphoprotein / Proto-oncogene / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / MET receptor recycling ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / MET receptor recycling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / phagocytosis / basal plasma membrane / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / molecular function activator activity / receptor protein-tyrosine kinase / Negative regulation of MET activity / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell migration / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / postsynapse / receptor complex / cell surface receptor signaling pathway / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bellon, S.F. / Albrecht, B.K. / Harmange, J.-C. / Bauer, D. / Choquette, D. / Dussault, I. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Discovery and Optimization of Triazolopyridazines as Potent and Selective Inhibitors of the c-Met Kinase. Authors: Albrecht, B.K. / Harmange, J.C. / Bauer, D. / Berry, L. / Bode, C. / Boezio, A.A. / Chen, A. / Choquette, D. / Dussault, I. / Fridrich, C. / Hirai, S. / Hoffman, D. / Larrow, J.F. / Kaplan- ...Authors: Albrecht, B.K. / Harmange, J.C. / Bauer, D. / Berry, L. / Bode, C. / Boezio, A.A. / Chen, A. / Choquette, D. / Dussault, I. / Fridrich, C. / Hirai, S. / Hoffman, D. / Larrow, J.F. / Kaplan-Lefko, P. / Lin, J. / Lohman, J. / Long, A.M. / Moriguchi, J. / O'Connor, A. / Potashman, M.H. / Reese, M. / Rex, K. / Siegmund, A. / Shah, K. / Shimanovich, R. / Springer, S.K. / Teffera, Y. / Yang, Y. / Zhang, Y. / Bellon, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cd8.cif.gz | 73.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cd8.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cd8_validation.pdf.gz | 787 KB | Display | wwPDB validaton report |
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Full document | 3cd8_full_validation.pdf.gz | 789.3 KB | Display | |
Data in XML | 3cd8_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 3cd8_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/3cd8 ftp://data.pdbj.org/pub/pdb/validation_reports/cd/3cd8 | HTTPS FTP |
-Related structure data
Related structure data | 3ccnC 2rfnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35346.910 Da / Num. of mol.: 1 / Fragment: protein kinase domain, c-Met kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P08581, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-L5G / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.8 Details: 0.1M HEPES pH 7.8, 15% PEG 4K, 6% 2-Propanol, 40mM BME, and 3% Ethanol, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 24, 2006 / Details: varimax optics |
Radiation | Monochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20427 / Num. obs: 19263 / % possible obs: 94.3 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1587 / % possible all: 78.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RFN Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.938 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.251 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.191 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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