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Open data
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Basic information
Entry | Database: PDB / ID: 7ybx | ||||||||||||
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Title | Crystal structure of FGFR4(V550M) kinase domain with 10z | ||||||||||||
![]() | Fibroblast growth factor receptor 4 | ||||||||||||
![]() | TRANSFERASE/INHIBITOR / Kinase / Inhibitor / STRUCTURAL PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||||||||
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 | ![]() ![]() | ||||||||||||
![]() | Chen, X.J. / Lin, Q.M. / Chen, Y.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Design, Synthesis, and Biological Evaluation of 5-Formyl-pyrrolo[3,2- b ]pyridine-3-carboxamides as New Selective, Potent, and Reversible-Covalent FGFR4 Inhibitors. Authors: Yang, F. / Chen, X. / Song, X. / Ortega, R. / Lin, X. / Deng, W. / Guo, J. / Tu, Z. / Patterson, A.V. / Smaill, J.B. / Chen, Y. / Lu, X. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.3 KB | Display | ![]() |
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PDB format | ![]() | 57 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.5 KB | Display | ![]() |
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Full document | ![]() | 757.6 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yboC ![]() 7ybpC ![]() 7yc1C ![]() 7yc3C ![]() 7wctS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34540.895 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: V550M,R664E 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-IH7 / ~{ | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.587 Å / Relative weight: 1 |
Reflection | Resolution: 2.233→42.823 Å / Num. obs: 14877 / % possible obs: 99.67 % / Redundancy: 7.3 % / Biso Wilson estimate: 22.4 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.2216 / Net I/σ(I): 9.75 |
Reflection shell | Resolution: 2.233→2.313 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 6.08 / Num. unique obs: 1436 / CC1/2: 0.934 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WCT Resolution: 2.233→42.823 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 21.72 / 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 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.81 Å2 / Biso mean: 27.0086 Å2 / Biso min: 8.39 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.233→42.823 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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