+Open data
-Basic information
Entry | Database: PDB / ID: 2of4 | ||||||
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Title | crystal structure of furanopyrimidine 1 bound to lck | ||||||
Components | Proto-oncogene tyrosine-protein kinase LCK | ||||||
Keywords | TRANSFERASE / lck / kinase domain | ||||||
Function / homology | Function and homology information regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / Interleukin-2 signaling ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / Interleukin-2 signaling / CD28 dependent Vav1 pathway / positive regulation of heterotypic cell-cell adhesion / protein serine/threonine phosphatase activity / Regulation of KIT signaling / CTLA4 inhibitory signaling / leukocyte migration / phospholipase activator activity / positive regulation of T cell receptor signaling pathway / pericentriolar material / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / PECAM1 interactions / phospholipase binding / CD28 dependent PI3K/Akt signaling / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / CD8 receptor binding / PD-1 signaling / phosphatidylinositol 3-kinase binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / GPVI-mediated activation cascade / T cell costimulation / extrinsic component of cytoplasmic side of plasma membrane / phosphotyrosine residue binding / SH2 domain binding / T cell receptor binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / activation of cysteine-type endopeptidase activity involved in apoptotic process / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of T cell activation / Downstream TCR signaling / PIP3 activates AKT signaling / DAP12 signaling / ATPase binding / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / protein phosphorylation / signaling receptor binding / innate immune response / protein kinase binding / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Martin, M.W. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Discovery of novel 2,3-diarylfuro[2,3-b]pyridin-4-amines as potent and selective inhibitors of Lck: Synthesis, SAR, and pharmacokinetic properties. Authors: Martin, M.W. / Newcomb, J. / Nunes, J.J. / Bemis, J.E. / McGowan, D.C. / White, R.D. / Buchanan, J.L. / Dimauro, E.F. / Boucher, C. / Faust, T. / Hsieh, F. / Huang, X. / Lee, J.H. / ...Authors: Martin, M.W. / Newcomb, J. / Nunes, J.J. / Bemis, J.E. / McGowan, D.C. / White, R.D. / Buchanan, J.L. / Dimauro, E.F. / Boucher, C. / Faust, T. / Hsieh, F. / Huang, X. / Lee, J.H. / Schneider, S. / Turci, S.M. / Zhu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2of4.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2of4.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 2of4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/2of4 ftp://data.pdbj.org/pub/pdb/validation_reports/of/2of4 | HTTPS FTP |
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-Related structure data
Related structure data | 2of2C 1qpcS 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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Unit cell |
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Details | The biological assembly is a monomer as observed. |
-Components
#1: Protein | Mass: 31345.889 Da / Num. of mol.: 1 / Fragment: lck kinase domain, residues 230-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCK / Production host: Insect cell References: UniProt: P06239, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-979 / |
#3: 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: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Li2SO4, 25-35% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→100 Å / Num. all: 8343 / Num. obs: 7392 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3 / % possible all: 58.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPC Resolution: 2.7→100 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→100 Å
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Refine LS restraints |
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