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Yorodumi- PDB-2xp2: Structure of the Human Anaplastic Lymphoma Kinase in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xp2 | ||||||
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Title | Structure of the Human Anaplastic Lymphoma Kinase in Complex with Crizotinib (PF-02341066) | ||||||
Components | TYROSINE-PROTEIN KINASE RECEPTOR | ||||||
Keywords | TRANSFERASE / CRIZOTINIB | ||||||
Function / homology | Function and homology information response to environmental enrichment / 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 / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...response to environmental enrichment / 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 / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / ALK mutants bind TKIs / swimming behavior / positive regulation of dendrite development / regulation of neuron differentiation / adult behavior / Signaling by ALK / Signaling by ALK fusions and activated point mutants / neuron development / Nuclear events stimulated by ALK signaling in cancer / negative regulation of lipid catabolic process / energy homeostasis / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / hippocampus development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / heparin binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / protein tyrosine kinase activity / regulation of apoptotic process / protein autophosphorylation / receptor complex / phosphorylation / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | McTigue, M. / Deng, Y. / Liu, W. / Brooun, A. / Timofeevski, S. / Marrone, T. / Cui, J.J. | ||||||
Citation | Journal: J.Med.Chem / Year: 2011 Title: Structure Based Drug Design of Crizotinib (Pf-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal-Epithelial Transition Factor (C-met) Kinase and Anaplastic Lymphoma Kinase (Alk). Authors: Cui, J.J. / Tran-Dube, M. / Shen, H. / Nambu, M. / Kung, P.P. / Pairish, M. / Jia, L. / Meng, J. / Funk, L. / Botrous, I. / Mctigue, M. / Grodsky, N. / Ryan, K. / Padrique, E. / Alton, G. / ...Authors: Cui, J.J. / Tran-Dube, M. / Shen, H. / Nambu, M. / Kung, P.P. / Pairish, M. / Jia, L. / Meng, J. / Funk, L. / Botrous, I. / Mctigue, M. / Grodsky, N. / Ryan, K. / Padrique, E. / Alton, G. / Timofeevski, S. / Yamazaki, S. / Li, Q. / Zou, H. / Christensen, J. / Mroczkowski, B. / Bender, S. / Kania, R.S. / Edwards, M.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xp2.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xp2.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xp2 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xp2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wgjSC 2wkmC S: Starting model for refinement C: citing same article (ref.) |
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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: 36909.355 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN, RESIDUES 105-423 Source method: isolated from a genetically manipulated source Details: NONPHOSPHORYLATED / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: B6EXY4, UniProt: Q9UM73*PLUS, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-VGH / |
#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: 1.99 Å3/Da / Density % sol: 38.5 % / Description: NONE |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: CO-CRYSTALS OF ALK KINASE DOMAIN WITH PF-02341066 WERE OBTAINED AT 13 DEGREES C BY USING HANGING-DROP VAPOR-DIFFUSION. 0.5 MICROLITERS OF 1:3 MOLAR RATIO OF 14.9 MG/ML PROTEIN SOLUTION TO ...Details: CO-CRYSTALS OF ALK KINASE DOMAIN WITH PF-02341066 WERE OBTAINED AT 13 DEGREES C BY USING HANGING-DROP VAPOR-DIFFUSION. 0.5 MICROLITERS OF 1:3 MOLAR RATIO OF 14.9 MG/ML PROTEIN SOLUTION TO PF02341066 WAS MIXED WITH 0.5 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 7-10% (W/V) MEPEG 5K, 0.1M MES, PH6.0-6.5 AND 0.15M (NH4)2SO4. |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→104.71 Å / Num. obs: 24837 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WGJ Resolution: 1.9→36.76 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1420278.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.504 Å2 / ksol: 0.394755 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.76 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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