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Yorodumi- PDB-3lzb: EGFR kinase domain complexed with an imidazo[2,1-b]thiazole inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lzb | ||||||
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Title | EGFR kinase domain complexed with an imidazo[2,1-b]thiazole inhibitor | ||||||
Components | Epidermal growth factor receptor | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / epidermal growth factor kinase domain / multitargeted small molecule kinase inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / MAP kinase kinase kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / 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 / EGFR Transactivation by Gastrin / cellular response to cadmium ion / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Swinger, K.K. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Imidazo[2,1-b]thiazoles: multitargeted inhibitors of both the insulin-like growth factor receptor and members of the epidermal growth factor family of receptor tyrosine kinases. Authors: Fidanze, S.D. / Erickson, S.A. / Wang, G.T. / Mantei, R. / Clark, R.F. / Sorensen, B.K. / Bamaung, N.Y. / Kovar, P. / Johnson, E.F. / Swinger, K.K. / Stewart, K.D. / Zhang, Q. / Tucker, L.A. ...Authors: Fidanze, S.D. / Erickson, S.A. / Wang, G.T. / Mantei, R. / Clark, R.F. / Sorensen, B.K. / Bamaung, N.Y. / Kovar, P. / Johnson, E.F. / Swinger, K.K. / Stewart, K.D. / Zhang, Q. / Tucker, L.A. / Pappano, W.N. / Wilsbacher, J.L. / Wang, J. / Sheppard, G.S. / Bell, R.L. / Davidsen, S.K. / Hubbard, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lzb.cif.gz | 248.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lzb.ent.gz | 189.9 KB | Display | PDB format |
PDBx/mmJSON format | 3lzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lzb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 3lzb_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3lzb_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 3lzb_validation.cif.gz | 64.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/3lzb ftp://data.pdbj.org/pub/pdb/validation_reports/lz/3lzb | HTTPS FTP |
-Related structure data
Related structure data | 2gs7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36137.484 Da / Num. of mol.: 8 / Fragment: UNP residues 696-1022 / Mutation: V924R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi5 References: UniProt: P00533, receptor protein-tyrosine kinase #2: Chemical | ChemComp-ITI / #3: Water | ChemComp-HOH / | Sequence details | THE ACTUAL CRYSTALLIZED SEQUENCE FOR THE LAST 39 C-TERMINAL RESIDUES IS ...THE ACTUAL CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: 0.15M cesium chloride, 15% w/v polyethylene glycol 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2009 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 36061 / Num. obs: 36046 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 62.974 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 13.55 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3571 / Rsym value: 0.52 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GS7 Resolution: 2.7→44.17 Å / Cross valid method: THROUGHOUT / σ(F): 2.7 / σ(I): 2.7
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Displacement parameters | Biso mean: 57.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→44.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Total num. of bins used: 9
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