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Yorodumi- PDB-3bym: X-ray co-crystal structure aminobenzimidazole triazine 1 bound to Lck -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bym | ||||||
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Title | X-ray co-crystal structure aminobenzimidazole triazine 1 bound to Lck | ||||||
Components | Proto-oncogene tyrosine-protein kinase LCK | ||||||
Keywords | TRANSFERASE / Lck / kinase domain / Alternative splicing / ATP-binding / Chromosomal rearrangement / Cytoplasm / Disease mutation / Host-virus interaction / Lipoprotein / Membrane / Myristate / Nucleotide-binding / Palmitate / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Tyrosine-protein kinase | ||||||
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 / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / CD28 co-stimulation / FLT3 signaling through SRC family kinases / intracellular zinc ion homeostasis / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / Regulation of KIT signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / phospholipase activator activity / leukocyte migration / CD8 receptor binding / pericentriolar material / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / peptidyl-tyrosine autophosphorylation / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / hemopoiesis / RHOH GTPase cycle / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of intrinsic apoptotic signaling pathway / release of sequestered calcium ion into cytosol / cell surface receptor protein tyrosine kinase signaling pathway / GPVI-mediated activation cascade / T cell costimulation / phosphotyrosine residue binding / SH2 domain 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 / peptidyl-tyrosine phosphorylation / Signaling by SCF-KIT / platelet activation / activation of cysteine-type endopeptidase activity involved in apoptotic process / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / positive regulation of T cell activation / Downstream TCR signaling / DAP12 signaling / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / T cell receptor signaling pathway / protein phosphatase binding / protein tyrosine kinase activity / intracellular signal transduction / response to xenobiotic stimulus / membrane raft / protein phosphorylation / innate immune response / signaling receptor binding / 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 Å | ||||||
Authors | Huang, X. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): ...Title: Structure-based design of novel 2-amino-6-phenyl-pyrimido[5',4':5,6]pyrimido[1,2-a]benzimidazol-5(6H)-ones as potent and orally active inhibitors of lymphocyte specific kinase (Lck): synthesis, SAR, and in vivo anti-inflammatory activity. Authors: Martin, M.W. / Newcomb, J. / Nunes, J.J. / Boucher, C. / Chai, L. / Epstein, L.F. / Faust, T. / Flores, S. / Gallant, P. / Gore, A. / Gu, Y. / Hsieh, F. / Huang, X. / Kim, J.L. / Middleton, ...Authors: Martin, M.W. / Newcomb, J. / Nunes, J.J. / Boucher, C. / Chai, L. / Epstein, L.F. / Faust, T. / Flores, S. / Gallant, P. / Gore, A. / Gu, Y. / Hsieh, F. / Huang, X. / Kim, J.L. / Middleton, S. / Morgenstern, K. / Oliveira-dos-Santos, A. / Patel, V.F. / Powers, D. / Rose, P. / Tudor, Y. / Turci, S.M. / Welcher, A.A. / Zack, D. / Zhao, H. / Zhu, L. / Zhu, X. / Ghiron, C. / Ermann, M. / Johnston, D. / Saluste, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bym.cif.gz | 77.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bym.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bym_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
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Full document | 3bym_full_validation.pdf.gz | 471.7 KB | Display | |
Data in XML | 3bym_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 3bym_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/3bym ftp://data.pdbj.org/pub/pdb/validation_reports/by/3bym | HTTPS FTP |
-Related structure data
Related structure data | 3byoC 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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-Components
#1: Protein | Mass: 31553.994 Da / Num. of mol.: 1 / Fragment: kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCK / Cell line (production host): Insect Cell / Production host: Baculovirus References: UniProt: P06239, non-specific protein-tyrosine kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-AM0 / | #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: 2.27 Å3/Da / Density % sol: 45.88 % |
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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 |
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→30 Å / Num. all: 20108 / Num. obs: 19838 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.77 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 6.7 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPC Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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