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Yorodumi- PDB-6nvg: FGFR4 complex with N-(3,5-dichloro-2-((5-((2,6-dichloro-3,5-dimet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nvg | ||||||
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Title | FGFR4 complex with N-(3,5-dichloro-2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)phenyl)acrylamide | ||||||
Components | Fibroblast growth factor receptor 4 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex / TRANSFERASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Lin, X. / Smaill, J.B. / Squire, C.J. / Yosaatmadja, Y. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nvg.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nvg.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 6nvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nvg_validation.pdf.gz | 739.9 KB | Display | wwPDB validaton report |
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Full document | 6nvg_full_validation.pdf.gz | 740.9 KB | Display | |
Data in XML | 6nvg_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 6nvg_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/6nvg ftp://data.pdbj.org/pub/pdb/validation_reports/nv/6nvg | HTTPS FTP |
-Related structure data
Related structure data | 6nvhC 6nviC 6nvjC 6nvkC 6nvlC 4xcuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) 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 | #3: Chemical | ChemComp-XL8 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM Bis-tris pH4.5, 200mM Lithium sulphate, 16% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 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: 1.99→60.18 Å / Num. obs: 26662 / % possible obs: 99.4 % / Redundancy: 26.1 % / CC1/2: 1 / Rpim(I) all: 0.019 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 25 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1784 / CC1/2: 0.675 / Rpim(I) all: 0.433 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XCU Resolution: 1.99→60.18 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.161 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / 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: 45.557 Å2
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Refinement step | Cycle: 1 / Resolution: 1.99→60.18 Å
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Refine LS restraints |
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