+Open data
-Basic information
Entry | Database: PDB / ID: 7vkn | ||||||
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Title | Crystal structure of TrkA (G595R) kinase with repotrectinib | ||||||
Components | Tyrosine-protein kinase receptor | ||||||
Keywords | TRANSFERASE / TRK / NTRK / macrocyclic inhibitor / drug resistance / repotrectinib | ||||||
Function / homology | Function and homology information neurotrophin receptor activity / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase / nervous system development / cell differentiation / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Murray, B.W. / Rogers, E. / Zhai, D. / Deng, W. / Chen, X. / Sprengeler, P.A. / Zhang, X. / Graber, A. / Reich, S.H. / Stopatschinskaja, S. ...Murray, B.W. / Rogers, E. / Zhai, D. / Deng, W. / Chen, X. / Sprengeler, P.A. / Zhang, X. / Graber, A. / Reich, S.H. / Stopatschinskaja, S. / Solomon, B. / Besse, B. / Drilon, A. | ||||||
Funding support | 1items
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Citation | Journal: Mol.Cancer Ther. / Year: 2021 Title: Molecular Characteristics of Repotrectinib That Enable Potent Inhibition of TRK Fusion Proteins and Resistant Mutations. Authors: Murray, B.W. / Rogers, E. / Zhai, D. / Deng, W. / Chen, X. / Sprengeler, P.A. / Zhang, X. / Graber, A. / Reich, S.H. / Stopatschinskaja, S. / Solomon, B. / Besse, B. / Drilon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vkn.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vkn.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkn ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkn | HTTPS FTP |
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-Related structure data
Related structure data | 7vkmC 7vkoC 4yneS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37335.922 Da / Num. of mol.: 1 / Mutation: G595R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: J3KP20, receptor protein-tyrosine kinase | ||||
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#2: Chemical | ChemComp-7GI / | ||||
#3: Chemical | ChemComp-SO4 / #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: 2.94 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.0M NaCl, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19.94 Å / Num. obs: 11040 / % possible obs: 90.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.7→2.83 Å / Rmerge(I) obs: 0.478 / Num. unique obs: 1439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4yne Resolution: 2.7→19.95 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.215 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.982 / ESU R Free: 0.353 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.034 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→19.95 Å
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Refine LS restraints |
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