[English] 日本語
![](img/lk-miru.gif)
- PDB-8a2a: EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a2a | ||||||
---|---|---|---|---|---|---|---|
Title | EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2-[4-[[4-(hydroxymethyl)-1-piperidyl]methyl]phenyl]ethynyl]-1-oxo-4-(trifluoromethyl)isoindolin-2-yl]-N-thiazol-2-yl-acetamide (form 2) | ||||||
![]() | Epidermal growth factor receptor | ||||||
![]() | TRANSFERASE / KINASE INHIBITOR | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Ehler, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Discovery of Novel Allosteric EGFR L858R Inhibitors for the Treatment of Non-Small-Cell Lung Cancer as a Single Agent or in Combination with Osimertinib. Authors: Obst-Sander, U. / Ricci, A. / Kuhn, B. / Friess, T. / Koldewey, P. / Kuglstatter, A. / Hewings, D. / Goergler, A. / Steiner, S. / Rueher, D. / Imhoff, M.P. / Raschetti, N. / Marty, H.P. / ...Authors: Obst-Sander, U. / Ricci, A. / Kuhn, B. / Friess, T. / Koldewey, P. / Kuglstatter, A. / Hewings, D. / Goergler, A. / Steiner, S. / Rueher, D. / Imhoff, M.P. / Raschetti, N. / Marty, H.P. / Dietzig, A. / Rynn, C. / Ehler, A. / Burger, D. / Kornacker, M. / Schaffland, J.P. / Herting, F. / Pao, W. / Bischoff, J.R. / Martoglio, B. / Alice Nagel, Y. / Jaeschke, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 145.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8a27SC ![]() 8a2bC ![]() 8a2dC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 37225.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, receptor protein-tyrosine kinase |
---|---|
#2: Chemical | ChemComp-KY9 / ( |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.74 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG Smear Medium, 0.1 M sodium cacodylate, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→68.59 Å / Num. obs: 40957 / % possible obs: 94.5 % / Redundancy: 10.3 % / CC1/2: 1 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.43→1.58 Å / Num. unique obs: 2156 / CC1/2: 0.67 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8A27 Resolution: 1.43→57.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.066 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 100.11 Å2 / Biso mean: 30.325 Å2 / Biso min: 12.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.43→57.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.43→1.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 4.0271 Å / Origin y: -8.7772 Å / Origin z: -14.3764 Å
|