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- PDB-5ur1: FGFR1 kinase domain complex with SN37333 in reversible binding mode -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ur1 | ||||||
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Title | FGFR1 kinase domain complex with SN37333 in reversible binding mode | ||||||
![]() | Fibroblast growth factor receptor 1![]() | ||||||
![]() | transferase/transferase inhibitor / ![]() | ||||||
Function / homology | ![]() Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yosaatmadja, Y. / Paik, W.-K. / Smaill, J.B. / Squire, C.J. | ||||||
![]() | ![]() Title: 2-Oxo-3, 4-dihydropyrimido[4, 5-d]pyrimidinyl derivatives as new irreversible pan fibroblast growth factor receptor (FGFR) inhibitors. Authors: Li, X. / Guise, C.P. / Taghipouran, R. / Yosaatmadja, Y. / Ashoorzadeh, A. / Paik, W.K. / Squire, C.J. / Jiang, S. / Luo, J. / Xu, Y. / Tu, Z.C. / Lu, X. / Ren, X. / Patterson, A.V. / Smaill, J.B. / Ding, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 227.6 KB | Display | ![]() |
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PDB format | ![]() | 181.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wunS ![]() 5uok ![]() 5uol ![]() 5uom ![]() 5uon 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 35353.613 Da / Num. of mol.: 2 / Mutation: C488A, C584S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P11362, ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% MPEG 5000, 0.1 M sodium cacodylate pH 7.5, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→19.54 Å / Num. obs: 35322 / % possible obs: 99.8 % / Redundancy: 14.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.041 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 15 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3440 / Num. unique obs: 3248 / CC1/2: 0.736 / Rpim(I) all: 0.349 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4WUN Resolution: 2.2→19.54 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 17.593 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.735 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→19.54 Å
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Refine LS restraints |
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