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Yorodumi- PDB-7jyr: hALK in complex with 1-[(1R,2R)-1-(2,4-difluorophenyl)-2-[2-(5-me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jyr | ||||||
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Title | hALK in complex with 1-[(1R,2R)-1-(2,4-difluorophenyl)-2-[2-(5-methyl-1H-pyrazol-3-yl)-4-(trifluoromethyl)phenoxy]cyclopropyl]methanamine | ||||||
Components | ALK tyrosine kinase receptor | ||||||
Keywords | TRANSFERASE / ALK tyrosine kinase receptor / INHIBITOR / COMPLEX / KINASE / SBDD / TRANSFERASE-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / swimming behavior / positive regulation of dendrite development / regulation of neuron differentiation / Signaling by ALK / adult behavior / peptidyl-tyrosine autophosphorylation / neuron development / transmembrane receptor protein tyrosine kinase activity / negative regulation of lipid catabolic process / energy homeostasis / cell surface receptor protein tyrosine kinase signaling pathway / phosphorylation / hippocampus development / receptor protein-tyrosine kinase / Signaling by ALK fusions and activated point mutants / positive regulation of NF-kappaB transcription factor activity / heparin binding / regulation of cell population proliferation / protein tyrosine kinase activity / regulation of apoptotic process / protein autophosphorylation / receptor complex / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | McGrath, A.P. / Zou, H. / Lane, W. / Saikatendu, K. | ||||||
Citation | Journal: Acs Omega / Year: 2020 Title: Discovery of Novel and Highly Selective Cyclopropane ALK Inhibitors through a Fragment-Assisted, Structure-Based Drug Design. Authors: Fujimori, I. / Wakabayashi, T. / Murakami, M. / Okabe, A. / Ishii, T. / McGrath, A. / Zou, H. / Saikatendu, K.S. / Imoto, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jyr.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jyr.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/7jyr ftp://data.pdbj.org/pub/pdb/validation_reports/jy/7jyr | HTTPS FTP |
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-Related structure data
Related structure data | 7jy4C 7jysC 7jytC 4z55S 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: 36045.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Plasmid: pFastBacHTb / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9UM73, receptor protein-tyrosine kinase | ||||
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#2: Chemical | ChemComp-VTA / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18.25% PEG 3350, 2.0% Tacsimate pH 7.0, 0.09M Tris Cl, 0.01M Tris base |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→29.48 Å / Num. obs: 70665 / % possible obs: 97.51 % / Redundancy: 5.3 % / Biso Wilson estimate: 42.12 Å2 / Rmerge(I) obs: 0.1164 / Net I/σ(I): 16.16 |
Reflection shell | Resolution: 2.322→2.405 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6387 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 3680 / % possible all: 81.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4z55 Resolution: 2.32→29.48 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.32→29.48 Å
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