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- PDB-4ymj: (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Clas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ymj | ||||||
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Title | (R)-2-Phenylpyrrolidine Substitute Imidazopyridazines: a New Class of Potent and Selective Pan-TRK Inhibitors | ||||||
![]() | NT-3 growth factor receptor | ||||||
![]() | Transferase/Transferase inhibitor / Kinase / TRK / Inhibitor / Oncology / Transferase-Transferase inhibitor complex | ||||||
Function / homology | ![]() NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / Receptor-type tyrosine-protein phosphatases / NTRK3 as a dependence receptor / neurotrophin receptor activity / neurotrophin binding / Activated NTRK3 signals through PI3K / activation of GTPase activity / positive regulation of positive chemotaxis ...NTF3 activates NTRK3 signaling / Activated NTRK3 signals through PLCG1 / Signaling by NTRK3 (TRKC) / Receptor-type tyrosine-protein phosphatases / NTRK3 as a dependence receptor / neurotrophin receptor activity / neurotrophin binding / Activated NTRK3 signals through PI3K / activation of GTPase activity / positive regulation of positive chemotaxis / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Activated NTRK3 signals through RAS / cell surface receptor protein tyrosine kinase signaling pathway / activation of protein kinase B activity / transmembrane receptor protein tyrosine kinase activity / cellular response to nerve growth factor stimulus / negative regulation of protein phosphorylation / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / p53 binding / positive regulation of peptidyl-serine phosphorylation / nervous system development / heart development / cell differentiation / receptor complex / positive regulation of cell migration / positive regulation of protein phosphorylation / phosphorylation / axon / positive regulation of cell population proliferation / positive regulation of gene expression / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kreusch, A. / Rucker, P. / Molteni, V. / Loren, J. | ||||||
![]() | ![]() Title: (R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class of Potent and Selective Pan-TRK Inhibitors. Authors: Choi, H.S. / Rucker, P.V. / Wang, Z. / Fan, Y. / Albaugh, P. / Chopiuk, G. / Gessier, F. / Sun, F. / Adrian, F. / Liu, G. / Hood, T. / Li, N. / Jia, Y. / Che, J. / McCormack, S. / Li, A. / ...Authors: Choi, H.S. / Rucker, P.V. / Wang, Z. / Fan, Y. / Albaugh, P. / Chopiuk, G. / Gessier, F. / Sun, F. / Adrian, F. / Liu, G. / Hood, T. / Li, N. / Jia, Y. / Che, J. / McCormack, S. / Li, A. / Li, J. / Steffy, A. / Culazzo, A. / Tompkins, C. / Phung, V. / Kreusch, A. / Lu, M. / Hu, B. / Chaudhary, A. / Prashad, M. / Tuntland, T. / Liu, B. / Harris, J. / Seidel, H.M. / Loren, J. / Molteni, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253 KB | Display | ![]() |
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PDB format | ![]() | 201.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 799.9 KB | Display | ![]() |
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Full document | ![]() | 807.7 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yneC ![]() 4ypsC ![]() 3v5qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34727.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Sequence refers to NTRK3 isoform b precursor (NP_002521.2) Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16288, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.85 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 2.5 M NACL, 0.1 M NA/K PHOSPHATE PH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 49818 / % possible obs: 87.19 % / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.92→1.96 Å / Rmerge(I) obs: 0.73 / % possible all: 78.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3V5Q Resolution: 2→47.704 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.56 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.704 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -5.538 Å / Origin y: -9.0101 Å / Origin z: 11.0436 Å
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Refinement TLS group | Selection details: all |