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- PDB-6nvj: FGFR4 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: 6nvj | ||||||
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Title | FGFR4 complex with N-(2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)-3-fluorophenyl)acrylamide | ||||||
![]() | Fibroblast growth factor receptor 4 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE | ||||||
Function / homology | ![]() FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / fibroblast growth factor binding ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / positive regulation of DNA biosynthetic process / fibroblast growth factor binding / positive regulation of catalytic activity / PI-3K cascade:FGFR4 / positive regulation of proteolysis / regulation of lipid metabolic process / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / transport vesicle / FRS-mediated FGFR4 signaling / cholesterol homeostasis / Negative regulation of FGFR4 signaling / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / glucose homeostasis / heparin binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / receptor complex / endosome / positive regulation of cell population proliferation / positive regulation of gene expression / Golgi apparatus / endoplasmic reticulum / extracellular region / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, X. / Smaill, J.B. / Squire, C.J. / Yosaatmadja, Y. | ||||||
![]() | ![]() 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 | ![]() | 70.1 KB | Display | ![]() |
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PDB format | ![]() | 48.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 716.5 KB | Display | ![]() |
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Full document | ![]() | 716.2 KB | Display | |
Data in XML | ![]() | 11.5 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nvgC ![]() 6nvhC ![]() 6nviC ![]() 6nvkC ![]() 6nvlC ![]() 4xcuS 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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Unit cell |
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Components
#1: Protein | Mass: 33867.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22455, receptor protein-tyrosine kinase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-XL5 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM Bis-tris pH 4.5, 200mM Lithium sulphate, 16% PEG 3350 |
-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: Oct 14, 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: 2.3→59.57 Å / Num. obs: 17211 / % possible obs: 99.8 % / Redundancy: 28 % / CC1/2: 0.998 / Rpim(I) all: 0.051 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 27.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1619 / CC1/2: 0.498 / Rpim(I) all: 0.7 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4xcu Resolution: 2.3→59.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.261 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.229 / 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: 49.127 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→59.57 Å
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Refine LS restraints |
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