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Yorodumi- PDB-2zm3: Complex Structure of Insulin-like Growth Factor Receptor and Isoq... -
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-Basic information
Entry | Database: PDB / ID: 2zm3 | ||||||
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Title | Complex Structure of Insulin-like Growth Factor Receptor and Isoquinolinedione Inhibitor | ||||||
Components | Insulin-like growth factor 1 receptor | ||||||
Keywords | TRANSFERASE / IGFR / protein-inhibitor complex / tyrosine kinase / ATP-binding / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / protein kinase complex / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / insulin-like growth factor binding / protein transporter activity / IRS-related events triggered by IGF1R / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to aldosterone / cellular response to zinc ion starvation / insulin receptor complex / cellular response to testosterone stimulus / insulin-like growth factor I binding / transcytosis / insulin receptor activity / negative regulation of hepatocyte apoptotic process / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / insulin binding / response to L-glutamate / cellular response to insulin-like growth factor stimulus / establishment of cell polarity / positive regulation of axon regeneration / positive regulation of cytokinesis / positive regulation of osteoblast proliferation / amyloid-beta clearance / regulation of JNK cascade / Respiratory syncytial virus (RSV) attachment and entry / insulin receptor substrate binding / G-protein alpha-subunit binding / response to vitamin E / estrous cycle / negative regulation of MAPK cascade / SHC-related events triggered by IGF1R / phosphatidylinositol 3-kinase binding / peptidyl-tyrosine autophosphorylation / cellular response to transforming growth factor beta stimulus / T-tubule / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to dexamethasone stimulus / cerebellum development / insulin-like growth factor receptor signaling pathway / axonogenesis / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / response to nicotine / positive regulation of smooth muscle cell proliferation / insulin receptor binding / receptor protein-tyrosine kinase / caveola / cellular response to mechanical stimulus / cellular response to amyloid-beta / cellular senescence / insulin receptor signaling pathway / positive regulation of cold-induced thermogenesis / protein tyrosine kinase activity / response to ethanol / protein autophosphorylation / positive regulation of MAPK cascade / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of cell migration / immune response / axon / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / negative regulation of apoptotic process / signal transduction / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xu, W. / Mayer, S.C. / Boschelli, F. / Johnson, M. / Dwyer, B. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Lead identification to generate isoquinolinedione inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment Authors: Mayer, S.C. / Banker, A.L. / Boschelli, F. / Di, L. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Kutterer, K. / Moy, F. / Petusky, S. / Ravi, M. / Tkach, D. / Tsou, H.R. / Xu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zm3.cif.gz | 257 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zm3.ent.gz | 208.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zm3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 2zm3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2zm3_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 2zm3_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/2zm3 ftp://data.pdbj.org/pub/pdb/validation_reports/zm/2zm3 | HTTPS FTP |
-Related structure data
Related structure data | 1jqhS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35342.145 Da / Num. of mol.: 4 / Fragment: UNP residues 981-1286, IGF-1R Kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R References: UniProt: P08069, receptor protein-tyrosine kinase #2: Chemical | ChemComp-575 / ( #3: Water | ChemComp-HOH / | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris-HCl, pH8, 2M NaCl, 13-16% PEG6K, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 143 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 60396 / % possible obs: 90.8 % / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.45→2.56 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5939 / Rsym value: 0.462 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JQH Resolution: 2.5→46.37 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 32.81 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.37 Å
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Refine LS restraints |
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