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Yorodumi- PDB-4pp9: ITK kinase domain with compound 1 (N-[1-(3-CYANOBENZYL)-1H-PYRAZO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pp9 | ||||||
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Title | ITK kinase domain with compound 1 (N-[1-(3-CYANOBENZYL)-1H-PYRAZOL-4-YL]-2H-INDAZOLE-3-CARBOXAMIDE) | ||||||
Components | Tyrosine-protein kinase ITK/TSK | ||||||
Keywords | transferase/transferase inhibitor / protein kinase / phospho-transfer / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase ...gamma-delta T cell activation / NK T cell differentiation / activation of phospholipase C activity / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / phosphorylation / signal transduction / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Eigenbrot, C. / Shia, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Discovery and optimization of indazoles as potent and selective interleukin-2 inducible T cell kinase (ITK) inhibitors. Authors: Pastor, R.M. / Burch, J.D. / Magnuson, S. / Ortwine, D.F. / Chen, Y. / De La Torre, K. / Ding, X. / Eigenbrot, C. / Johnson, A. / Liimatta, M. / Liu, Y. / Shia, S. / Wang, X. / Wu, L.C. / Pei, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pp9.cif.gz | 210.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pp9.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4pp9 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4pp9 | HTTPS FTP |
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-Related structure data
Related structure data | 4ppaC 4ppbC 4ppcC 1sm2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30214.492 Da / Num. of mol.: 2 / Fragment: kinase domain / Mutation: Y512E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITK, EMT, LYK / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q08881, non-specific protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.76 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: sodium nitrate, PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 380K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 17994 / Num. obs: 17975 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 48.64 Å2 / Rsym value: 0.148 / Net I/σ(I): 7.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SM2 Resolution: 2.58→25.34 Å / Cor.coef. Fo:Fc: 0.9064 / Cor.coef. Fo:Fc free: 0.8591 / SU R Cruickshank DPI: 0.903 Isotropic thermal model: individual atomic plus TLS in two groups Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 44.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→25.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.74 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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