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Yorodumi- PDB-7vre: The crystal structure of EGFR T790M/C797S with the inhibitor HCD2892 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vre | ||||||
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Title | The crystal structure of EGFR T790M/C797S with the inhibitor HCD2892 | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / EGFR / inhibitor / complex / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / Resolution: 2.507 Å | ||||||
Authors | Zhu, S.J. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Conformational Constrained 4-(1-Sulfonyl-3-indol)yl-2-phenylaminopyrimidine Derivatives as New Fourth-Generation Epidermal Growth Factor Receptor Inhibitors Targeting T790M/C797S Mutations. Authors: Chen, H. / Lai, M. / Zhang, T. / Chen, Y. / Tong, L. / Zhu, S. / Zhou, Y. / Ren, X. / Ding, J. / Xie, H. / Lu, X. / Ding, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vre.cif.gz | 79.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vre.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/7vre ftp://data.pdbj.org/pub/pdb/validation_reports/vr/7vre | HTTPS FTP |
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-Related structure data
Related structure data | 7vraC 6j6r 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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Unit cell |
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-Components
#1: Protein | Mass: 37460.363 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-7VH / |
#3: 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: 3.48 Å3/Da / Density % sol: 64.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M HEPES pH 8.5, 40% PEG 400, 0.15 M NaCl, 5 mM tris(2-carboxyethyl)-phosphine (TCEP) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 18001 / % possible obs: 100 % / Redundancy: 19.5 % / Rpim(I) all: 0.055 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique obs: 18001 / Rpim(I) all: 0.762 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J6R 6j6r Resolution: 2.507→25.853 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.63 / 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: 125.35 Å2 / Biso mean: 69.2874 Å2 / Biso min: 38.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.507→25.853 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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