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- PDB-6nvl: FGFR1 complex with N-(2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)ox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nvl | ||||||
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Title | FGFR1 complex with N-(2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)-3-methylphenyl)acrylamide | ||||||
![]() | Fibroblast growth factor receptor 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE | ||||||
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 / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / cellular response to fibroblast growth factor stimulus / outer ear morphogenesis / middle ear morphogenesis / skeletal system morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / positive regulation of endothelial cell chemotaxis / ureteric bud development / midbrain development / inner ear morphogenesis / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / regulation of cell differentiation / phosphatidylinositol-mediated signaling / PI3K Cascade / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / : / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / SH2 domain binding / stem cell proliferation / Signal transduction by L1 / skeletal system development / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / positive regulation of MAP kinase activity / neuron migration / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / neuron projection development / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, X. / Smaill, J.B. / Squire, C.J. | ||||||
![]() | ![]() Title: Rotational Freedom, Steric Hindrance, and Protein Dynamics Explain BLU554 Selectivity for the Hinge Cysteine of FGFR4. Authors: Lin, X. / Yosaatmadja, Y. / Kalyukina, M. / Middleditch, M.J. / Zhang, Z. / Lu, X. / Ding, K. / Patterson, A.V. / Smaill, J.B. / Squire, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.5 KB | Display | ![]() |
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PDB format | ![]() | 175 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 37.3 KB | Display | |
Data in CIF | ![]() | 50.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nvgC ![]() 6nvhC ![]() 6nviC ![]() 6nvjC ![]() 6nvkC ![]() 4wunS 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35167.406 Da / Num. of mol.: 4 / Mutation: C584S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11362, receptor protein-tyrosine kinase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-XL6 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 90 mM NPS salt mixture (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfatesulfate), 100 mM HEPES/MOPS pH 7.5, and 50% v/v of a precipitant mixture of 40% v/v PEG ...Details: 90 mM NPS salt mixture (30 mM sodium nitrate, 30 mM sodium phosphate dibasic, 30 mM ammonium sulfatesulfate), 100 mM HEPES/MOPS pH 7.5, and 50% v/v of a precipitant mixture of 40% v/v PEG 500 MME and 20 % w/v PEG 20,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.06 Å / Num. obs: 40011 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.971 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.7→2.81 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4482 / CC1/2: 0.505 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WUN Resolution: 2.7→47.06 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.886 / SU B: 13.836 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.802 / ESU R Free: 0.339 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.898 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→47.06 Å
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Refine LS restraints |
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