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- PDB-3f5p: Complex Structure of Insulin-like Growth Factor Receptor and 3-Cy... -
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Basic information
Entry | Database: PDB / ID: 3f5p | ||||||
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Title | Complex Structure of Insulin-like Growth Factor Receptor and 3-Cyanoquinoline Inhibitor | ||||||
![]() | Insulin-like growth factor 1 receptor | ||||||
![]() | TRANSFERASE / IGF-1R / protein-inhibitor complex / tyrosine kinase / ATP-binding / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
Function / homology | ![]() cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / protein transporter activity / negative regulation of muscle cell apoptotic process ...cardiac atrium development / negative regulation of cholangiocyte apoptotic process / insulin-like growth factor receptor activity / positive regulation of steroid hormone biosynthetic process / protein kinase complex / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / protein transporter activity / negative regulation of muscle cell apoptotic process / cellular response to progesterone stimulus / positive regulation of DNA metabolic process / cellular response to zinc ion starvation / cellular response to aldosterone / insulin receptor complex / cellular response to testosterone stimulus / negative regulation of hepatocyte apoptotic process / insulin-like growth factor I binding / insulin receptor activity / transcytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / response to alkaloid / cellular response to angiotensin / positive regulation of protein-containing complex disassembly / dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / insulin binding / response to L-glutamate / negative regulation of MAPK cascade / establishment of cell polarity / positive regulation of axon regeneration / amyloid-beta clearance / positive regulation of osteoblast proliferation / positive regulation of cytokinesis / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / insulin receptor substrate binding / estrous cycle / G-protein alpha-subunit binding / response to vitamin E / 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 / axonogenesis / insulin-like growth factor receptor signaling pathway / caveola / cellular response to estradiol stimulus / hippocampus development / cellular response to glucose stimulus / positive regulation of smooth muscle cell proliferation / insulin receptor binding / response to nicotine / receptor protein-tyrosine kinase / 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 / positive regulation of MAPK cascade / protein autophosphorylation / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, W. / Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F. | ||||||
![]() | ![]() Title: Lead identification to generate 3-cyanoquinoline inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment Authors: Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F. / Di, L. / Du, X. / Dutia, M. / Floyd, M.B. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Moy, F. / Petusky, S. ...Authors: Miller, L.M. / Mayer, S.C. / Berger, D.M. / Boschelli, D.H. / Boschelli, F. / Di, L. / Du, X. / Dutia, M. / Floyd, M.B. / Johnson, M. / Kenny, C.H. / Krishnamurthy, G. / Moy, F. / Petusky, S. / Tkach, D. / Torres, N. / Wu, B. / Xu, W. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 937.9 KB | Display | ![]() |
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PDB format | ![]() | 787.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zm3S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 35342.145 Da / Num. of mol.: 16 / Fragment: IGF-1R Kinase Domain, UNP residues 981-1286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P08069, receptor protein-tyrosine kinase #2: Chemical | ChemComp-741 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris-HCl, pH8.5, 2M NaCl, 14% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 143 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 137596 / Num. obs: 133523 / % possible obs: 97.04 % / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 2.9→3 Å / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 2.67 / % possible all: 89.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ZM3 Resolution: 2.9→19.986 Å / SU ML: 0.44 / Isotropic thermal model: isotropic / σ(F): 0.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.778 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.986 Å
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Refine LS restraints |
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LS refinement shell |
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