+Open data
-Basic information
Entry | Database: PDB / ID: 7ukw | ||||||
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Title | EGFR(T790M/V948R) in complex with Lazertinib (YH25448) | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE / Cancer / Drug Design / EGFR / Signal Transduction / Targeted Therapy | ||||||
Function / homology | Function and homology information Complex I biogenesis / Respiratory electron transport / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / electron transfer activity / mitochondrial inner membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Pham, C.D. / Heppner, D.E. | ||||||
Funding support | 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2022 Title: Structural Basis for Inhibition of Mutant EGFR with Lazertinib (YH25448). Authors: Heppner, D.E. / Wittlinger, F. / Beyett, T.S. / Shaurova, T. / Urul, D.A. / Buckley, B. / Pham, C.D. / Schaeffner, I.K. / Yang, B. / Ogboo, B.C. / May, E.W. / Schaefer, E.M. / Eck, M.J. / ...Authors: Heppner, D.E. / Wittlinger, F. / Beyett, T.S. / Shaurova, T. / Urul, D.A. / Buckley, B. / Pham, C.D. / Schaeffner, I.K. / Yang, B. / Ogboo, B.C. / May, E.W. / Schaefer, E.M. / Eck, M.J. / Laufer, S.A. / Hershberger, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ukw.cif.gz | 250.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ukw.ent.gz | 200.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ukw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/7ukw ftp://data.pdbj.org/pub/pdb/validation_reports/uk/7ukw | HTTPS FTP |
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-Related structure data
Related structure data | 7ukvC 6wxnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37479.367 Da / Num. of mol.: 4 / Mutation: T790M, V948R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P00533, receptor protein-tyrosine kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG-3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2021 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.59→65.35 Å / Num. obs: 37527 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.47 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.106 / Rrim(I) all: 0.212 / Net I/σ(I): 4.8 / Num. measured all: 141225 / Scaling rejects: 326 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.8 %
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WXN Resolution: 2.6→65.35 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.76 Å2 / Biso mean: 44.6777 Å2 / Biso min: 14.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→65.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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