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- PDB-8fd9: Structure of BTK kinase domain with the second-generation inhibit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8fd9 | |||||||||
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Title | Structure of BTK kinase domain with the second-generation inhibitor acalabrutinib | |||||||||
![]() | Tyrosine-protein kinase BTK | |||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() negative regulation of B cell activation / G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / G alpha (12/13) signalling events / negative regulation of leukocyte proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / proteoglycan catabolic process ...negative regulation of B cell activation / G beta:gamma signalling through BTK / RHO GTPases Activate WASPs and WAVEs / FCERI mediated Ca+2 mobilization / G alpha (q) signalling events / G alpha (12/13) signalling events / negative regulation of leukocyte proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / proteoglycan catabolic process / monocyte proliferation / positive regulation of interleukin-17A production / 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 / negative regulation of cytokine production / DAP12 signaling / positive regulation of immunoglobulin production / positive regulation of NLRP3 inflammasome complex assembly / negative regulation of interleukin-10 production / phospholipase activator activity / negative regulation of B cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lin, D.Y. / Andreotti, A.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of BTK kinase domain with the second-generation inhibitors acalabrutinib and tirabrutinib. Authors: Lin, D.Y. / Andreotti, A.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.6 KB | Display | ![]() |
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PDB format | ![]() | 144.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ff0C 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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Unit cell |
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Components
#1: Protein | Mass: 31821.521 Da / Num. of mol.: 1 Mutation: K430R, L542M S543T, V555T, R562K, S564A, P565S, Y617P Source method: isolated from a genetically manipulated source Details: Bruton's Tyrosine Kinase in complex with acalabrutinib Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P35991, ![]() | ||||
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#2: Chemical | ChemComp-XQQ / | ||||
#3: Chemical | ChemComp-BR / ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow![]() | Temperature: 277 K / Method: evaporation / pH: 6.5 Details: 20% PEG 3350, 0.1M Bis-tris propane, pH 6.5 and 0.2M sodium bromide PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 7, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.626→46.591 Å / Num. obs: 28343 / % possible obs: 82.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.064 / Rrim(I) all: 0.162 / Net I/σ(I): 1.2 |
Reflection shell | Resolution: 1.626→1.745 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.276 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1418 / CC1/2: 0.499 / Rpim(I) all: 0.582 / % possible all: 21.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.74 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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