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Open data
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Basic information
Entry | Database: PDB / ID: 8d73 | ||||||
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Title | Crystal Structure of EGFR LRTM with compound 7 | ||||||
![]() | Epidermal growth factor receptor | ||||||
![]() | SIGNALING PROTEIN / Protein Kinase / inhibitor / kinase domain / mutation | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, J.L. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of BLU-945, a Reversible, Potent, and Wild-Type-Sparing Next-Generation EGFR Mutant Inhibitor for Treatment-Resistant Non-Small-Cell Lung Cancer. Authors: Eno, M.S. / Brubaker, J.D. / Campbell, J.E. / De Savi, C. / Guzi, T.J. / Williams, B.D. / Wilson, D. / Wilson, K. / Brooijmans, N. / Kim, J. / Ozen, A. / Perola, E. / Hsieh, J. / Brown, V. / ...Authors: Eno, M.S. / Brubaker, J.D. / Campbell, J.E. / De Savi, C. / Guzi, T.J. / Williams, B.D. / Wilson, D. / Wilson, K. / Brooijmans, N. / Kim, J. / Ozen, A. / Perola, E. / Hsieh, J. / Brown, V. / Fetalvero, K. / Garner, A. / Zhang, Z. / Stevison, F. / Woessner, R. / Singh, J. / Timsit, Y. / Kinkema, C. / Medendorp, C. / Lee, C. / Albayya, F. / Zalutskaya, A. / Schalm, S. / Dineen, T.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 157.9 KB | Display | ![]() |
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PDB format | ![]() | 120.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 32.7 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d76C ![]() 4i22S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 39797.777 Da / Num. of mol.: 2 / Mutation: T790M, L858R, V948R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.11 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.10 M sodium acetate, pH 5.8, 0.30 M potassium acetate, 15% glycerol, 9% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→29.8 Å / Num. obs: 31680 / % possible obs: 91.4 % / Redundancy: 1.7 % / Rrim(I) all: 0.13 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.17→2.29 Å / Redundancy: 1.7 % / Num. unique obs: 4458 / Rrim(I) all: 0.66 / % possible all: 88.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4i22 Resolution: 2.17→29.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.382 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.9 Å2 / Biso mean: 50.276 Å2 / Biso min: 21.09 Å2
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Refinement step | Cycle: final / Resolution: 2.17→29.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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