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- PDB-4rg0: Crystal structure of BTK kinase domain complexed with 2-[8-fluoro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rg0 | ||||||
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Title | Crystal structure of BTK kinase domain complexed with 2-[8-fluoro-2-[2-(hydroxymethyl)-3-[1-methyl-5-[[5-(4-methylpiperazin-1-yl)-2-pyridyl]amino]-6-oxo-3-pyridyl]phenyl]-1-oxo-3,4-dihydroisoquinolin-6-yl]-2-methyl-propanenitrile | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell ...regulation of B cell cytokine production / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / regulation of B cell apoptotic process / eosinophil homeostasis / positive regulation of type III hypersensitivity / B cell affinity maturation / positive regulation of synoviocyte proliferation / histamine secretion by mast cell / neutrophil homeostasis / cellular response to molecule of fungal origin / positive regulation of type I hypersensitivity / cellular response to interleukin-7 / MyD88 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of immunoglobulin production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-10 production / phospholipase activator activity / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Wong, A. | ||||||
![]() | ![]() Title: Finding the perfect spot for fluorine: Improving potency up to 40-fold during a rational fluorine scan of a Bruton's Tyrosine Kinase (BTK) inhibitor scaffold. Authors: Lou, Y. / Sweeney, Z.K. / Kuglstatter, A. / Davis, D. / Goldstein, D.M. / Han, X. / Hong, J. / Kocer, B. / Kondru, R.K. / Litman, R. / McIntosh, J. / Sarma, K. / Suh, J. / Taygerly, J. / Owens, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.6 KB | Display | ![]() |
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PDB format | ![]() | 94.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4rfyC ![]() 4rfzC ![]() 4otrS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32521.135 Da / Num. of mol.: 1 / Fragment: protein kinase domain (UNP residues 378-659) / Mutation: M489A, R492A, E624A, K625A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q06187, ![]() |
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#2: Chemical | ChemComp-3P0 / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 33% PEG3350, 0.1 M HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→42.76 Å / Num. obs: 9101 / % possible obs: 88.84 % / Redundancy: 3.4 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.141 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.5→2.565 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.459 / % possible all: 63.66 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4OTR Resolution: 2.5→42.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.868 / SU B: 26.712 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.479 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→42.76 Å
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Refine LS restraints |
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