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- PDB-4jq8: Crystal structure of EGFR kinase domain in complex with compound 4b -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jq8 | ||||||
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Title | Crystal structure of EGFR kinase domain in complex with compound 4b | ||||||
![]() | Epidermal growth factor receptor | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / Transferase / tyrosine kinase domain / ATP-binding domain / autophosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / EGFR Transactivation by Gastrin / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / ruffle membrane / positive regulation of miRNA transcription / cell-cell adhesion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peng, Y.H. / Wu, J.S. | ||||||
![]() | ![]() Title: Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors Authors: Peng, Y.H. / Shiao, H.Y. / Tu, C.H. / Liu, P.M. / Hsu, J.T. / Amancha, P.K. / Wu, J.S. / Coumar, M.S. / Chen, C.H. / Wang, S.Y. / Lin, W.H. / Sun, H.Y. / Chao, Y.S. / Lyu, P.C. / Hsieh, H.P. / Wu, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.2 KB | Display | ![]() |
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PDB format | ![]() | 108.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.2 KB | Display | ![]() |
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Full document | ![]() | 770.2 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jq7C ![]() 4jr3C ![]() 4jrvC ![]() 1m17S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37401.250 Da / Num. of mol.: 1 / Fragment: tyrosine kinase domain, UNP residues 696-1021 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00533, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-KJ8 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.0M Ammonium citrate tribase, 0.1M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→30 Å / Num. all: 12717 / Num. obs: 12717 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.05 |
Reflection shell | Resolution: 2.83→2.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 2.14 / Num. unique all: 1240 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1M17 Resolution: 2.83→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 25.419 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.61 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.045 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.829→2.903 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 156.67 Å / Origin y: 122.73 Å / Origin z: 205.772 Å
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