+Open data
-Basic information
Entry | Database: PDB / ID: 7ybo | ||||||||||||
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Title | Crystal structure of FGFR4 kinase domain with 10z | ||||||||||||
Components | Fibroblast growth factor receptor 4 | ||||||||||||
Keywords | TRANSFERASE/INHIBITOR / Kinase / Inhibitor / STRUCTURAL PROTEIN / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / fibroblast growth factor receptor activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / positive regulation of catalytic activity / positive regulation of DNA biosynthetic process ...FGFR4 mutant receptor activation / betaKlotho-mediated ligand binding / regulation of extracellular matrix disassembly / fibroblast growth factor receptor activity / phosphate ion homeostasis / regulation of bile acid biosynthetic process / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / positive regulation of catalytic activity / positive regulation of DNA biosynthetic process / fibroblast growth factor binding / 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 / FRS-mediated FGFR4 signaling / transport vesicle / 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 | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.307 Å | ||||||||||||
Authors | Chen, X.J. / Lin, Q.M. / Chen, Y.H. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Med.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ybo.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ybo.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ybo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ybo_validation.pdf.gz | 755 KB | Display | wwPDB validaton report |
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Full document | 7ybo_full_validation.pdf.gz | 759.3 KB | Display | |
Data in XML | 7ybo_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 7ybo_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/7ybo ftp://data.pdbj.org/pub/pdb/validation_reports/yb/7ybo | HTTPS FTP |
-Related structure data
Related structure data | 7ybpC 7ybxC 7yc1C 7yc3C 7wctS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34695.059 Da / Num. of mol.: 1 / Fragment: kinase domain / Mutation: R664E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR4, JTK2, TKF / Production host: Escherichia coli (E. coli) 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 | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.95 % |
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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: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.587 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 28, 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: 2.307→42.47 Å / Num. obs: 11880 / % possible obs: 93.64 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.43 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.1729 / Rrim(I) all: 0.1866 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 2.307→2.389 Å / Redundancy: 4 % / Rmerge(I) obs: 0.2879 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 769 / CC1/2: 0.907 / % possible all: 61.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WCT Resolution: 2.307→42.465 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.78 / 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: 88.11 Å2 / Biso mean: 37.0843 Å2 / Biso min: 22.33 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.307→42.465 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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