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- PDB-3pj1: Crystal structure of BTK kinase domain complexed with 3-(2,6-Dich... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pj1 | ||||||
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Title | Crystal structure of BTK kinase domain complexed with 3-(2,6-Dichloro-phenyl)-7-[4-(2-diethylamino-ethoxy)-phenylamino]-1-methyl-3,4-dihydro-1H-pyrimido[4,5-d]pyrimidin-2-one | ||||||
![]() | Tyrosine-protein kinase BTK | ||||||
![]() | TRANSFERASE/INHIBITOR / helix C-in / DFG-in / 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) / positive regulation of immunoglobulin production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of B cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / phospholipase activator activity / negative regulation of interleukin-10 production / B cell activation / negative regulation of B cell proliferation / Fc-epsilon receptor signaling pathway / mesoderm development / phosphatidylinositol-3,4,5-trisphosphate binding / phospholipase binding / RHO GTPases Activate WASPs and WAVEs / positive regulation of B cell proliferation / positive regulation of phagocytosis / cell maturation / FCERI mediated Ca+2 mobilization / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calcium-mediated signaling / apoptotic signaling pathway / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Regulation of actin dynamics for phagocytic cup formation / G beta:gamma signalling through BTK / cellular response to reactive oxygen species / peptidyl-tyrosine phosphorylation / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / G alpha (12/13) signalling events / DAP12 signaling / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / ER-Phagosome pathway / cytoplasmic vesicle / G alpha (q) signalling events / protein tyrosine kinase activity / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / intracellular signal transduction / membrane raft / protein phosphorylation / innate immune response / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuglstatter, A. / Wong, A. | ||||||
![]() | ![]() Title: Insights into the conformational flexibility of Bruton's tyrosine kinase from multiple ligand complex structures. Authors: Kuglstatter, A. / Wong, A. / Tsing, S. / Lee, S.W. / Lou, Y. / Villasenor, A.G. / Bradshaw, J.M. / Shaw, D. / Barnett, J.W. / Browner, M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 49.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 934 KB | Display | ![]() |
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Full document | ![]() | 937.3 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pixSC ![]() 3piyC ![]() 3pizC ![]() 3pj2C ![]() 3pj3C 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
#1: Protein | Mass: 31827.521 Da / Num. of mol.: 1 / Fragment: unp residues 387-659 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q06187, non-specific protein-tyrosine kinase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 33% PEG3350, 0.1M 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: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9804 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 20034 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rsym value: 0.135 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 1881 / Rsym value: 0.393 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PIX Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.137 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / 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: 24.717 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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