+Open data
-Basic information
Entry | Database: PDB / ID: 4pqn | ||||||
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Title | ITK kinase domain with compound GNE-9822 | ||||||
Components | Tyrosine-protein kinase ITK/TSK | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / phospho-transfer / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information : / NK T cell differentiation / gamma-delta T cell activation / Generation of second messenger molecules / cellular defense response / FCERI mediated Ca+2 mobilization / T cell activation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / B cell receptor signaling pathway ...: / NK T cell differentiation / gamma-delta T cell activation / Generation of second messenger molecules / cellular defense response / FCERI mediated Ca+2 mobilization / T cell activation / positive regulation of cytokine production / non-specific protein-tyrosine kinase / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / signal transduction / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | McEwan, P.A. / Barker, J.J. / Eigenbrot, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Property- and structure-guided discovery of a tetrahydroindazole series of interleukin-2 inducible T-cell kinase inhibitors. Authors: Burch, J.D. / Lau, K. / Barker, J.J. / Brookfield, F. / Chen, Y. / Chen, Y. / Eigenbrot, C. / Ellebrandt, C. / Ismaili, M.H. / Johnson, A. / Kordt, D. / MacKinnon, C.H. / McEwan, P.A. / ...Authors: Burch, J.D. / Lau, K. / Barker, J.J. / Brookfield, F. / Chen, Y. / Chen, Y. / Eigenbrot, C. / Ellebrandt, C. / Ismaili, M.H. / Johnson, A. / Kordt, D. / MacKinnon, C.H. / McEwan, P.A. / Ortwine, D.F. / Stein, D.B. / Wang, X. / Winkler, D. / Yuen, P.W. / Zhang, Y. / Zarrin, A.A. / Pei, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pqn.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pqn.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 4pqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pqn_validation.pdf.gz | 930.4 KB | Display | wwPDB validaton report |
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Full document | 4pqn_full_validation.pdf.gz | 941 KB | Display | |
Data in XML | 4pqn_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4pqn_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pqn ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pqn | HTTPS FTP |
-Related structure data
Related structure data | 4prjC 1sm2S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30116.418 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP residues 357-620 / Mutation: C477S,E614A,E617A 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 |
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#2: Chemical | ChemComp-2W6 / |
#3: Chemical | ChemComp-P4G / |
#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: 1.97 Å3/Da / Density % sol: 37.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: PEG6000, NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→50.6 Å / Num. all: 25458 / Num. obs: 25457 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SM2 Resolution: 1.71→50.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.856 / SU ML: 0.079 Isotropic thermal model: individual atomic plus TLS in one group Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.611 Å2
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Refine analyze | Luzzati coordinate error obs: 0.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→50.6 Å
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Refine LS restraints |
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