[English] 日本語
Yorodumi- PDB-8po0: Discovery and Optimisation of Potent, Efficacious and Selective I... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8po0 | ||||||
---|---|---|---|---|---|---|---|
Title | Discovery and Optimisation of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations. Compound 12 bound to EGFRinsNPG | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | SIGNALING PROTEIN / EGFR / Exon 20 insertion / non-small cell lung cancer / oncology | ||||||
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: 2.523 Å | ||||||
Authors | Hargreaves, D. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2024 Title: Discovery and Optimization of Potent, Efficacious and Selective Inhibitors Targeting EGFR Exon20 Insertion Mutations. Authors: Thomson, C. / Barton, P. / Braybrooke, E. / Colclough, N. / Dong, Z. / Evans, L. / Floc'h, N. / Guerot, C. / Hargreaves, D. / Khurana, P. / Li, S. / Li, X. / Lister, A. / McCoull, W. / ...Authors: Thomson, C. / Barton, P. / Braybrooke, E. / Colclough, N. / Dong, Z. / Evans, L. / Floc'h, N. / Guerot, C. / Hargreaves, D. / Khurana, P. / Li, S. / Li, X. / Lister, A. / McCoull, W. / McWilliams, L. / Orme, J.P. / Packer, M.J. / Swaih, A.M. / Ward, R.A. / Winlow, P. / Ye, Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8po0.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8po0.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 8po0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/8po0 ftp://data.pdbj.org/pub/pdb/validation_reports/po/8po0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8pnzC 8po1C 8po2C 8po3C 8po4C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37716.527 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 |
---|---|
#2: Chemical | ChemComp-2I6 / Mass: 459.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25N5O4 / Feature type: SUBJECT OF INVESTIGATION |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.79 Å3/Da / Density % sol: 67.51 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Sodium Citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1→47.68 Å / Num. obs: 19264 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 1 / Net I/σ(I): 1 |
Reflection shell | Resolution: 1→1 Å / Num. unique obs: 1 / CC1/2: 0.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.523→47.68 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.413 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.33 / SU Rfree Cruickshank DPI: 0.341
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 96.52 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.64 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.523→47.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.523→2.54 Å
|