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Yorodumi- PDB-4aua: Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6) -
+Open data
-Basic information
Entry | Database: PDB / ID: 4aua | ||||||
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Title | Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6) | ||||||
Components | CYCLIN-DEPENDENT KINASE 6 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation ...cyclin D2-CDK6 complex / cell dedifferentiation / Drug-mediated inhibition of CDK4/CDK6 activity / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / FBXO family protein binding / lateral ventricle development / negative regulation of myeloid cell differentiation / type B pancreatic cell development / negative regulation of monocyte differentiation / astrocyte development / dentate gyrus development / gliogenesis / regulation of cell motility / Regulation of RUNX1 Expression and Activity / regulation of hematopoietic stem cell differentiation / positive regulation of cell-matrix adhesion / generation of neurons / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of cellular senescence / negative regulation of cell differentiation / negative regulation of cell cycle / hematopoietic stem cell differentiation / cyclin-dependent protein kinase holoenzyme complex / negative regulation of osteoblast differentiation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Notch signaling pathway / ruffle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / : / response to virus / regulation of erythrocyte differentiation / Oncogene Induced Senescence / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / negative regulation of epithelial cell proliferation / positive regulation of fibroblast proliferation / T cell differentiation in thymus / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / regulation of cell cycle / negative regulation of cell population proliferation / cell division / protein phosphorylation / protein serine kinase activity / centrosome / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Cho, Y.S. / Angove, H. / Brain, C. / Chen, C.H.T. / Cheng, R. / Chopra, R. / Chung, K. / Congreve, M. / Dagostin, C. / Davis, D. ...Cho, Y.S. / Angove, H. / Brain, C. / Chen, C.H.T. / Cheng, R. / Chopra, R. / Chung, K. / Congreve, M. / Dagostin, C. / Davis, D. / Feltell, R. / Giraldes, J. / Hiscock, S. / Kim, S. / Kovats, S. / Lagu, B. / Lewry, K. / Loo, A. / Lu, Y. / Luzzio, M. / Maniara, W. / Mcmenamin, R. / Mortenson, P. / Benning, R. / O'Reilly, M. / Rees, D. / Shen, J. / Smith, T. / Wang, Y. / Williams, G. / Woolford, A. / Wrona, W. / Xu, M. / Yang, F. / Howard, S. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2012 Title: Fragment-Based Discovery of 7-Azabenzimidazoles as Potent, Highly Selective, and Orally Active CDK4/6 Inhibitors. Authors: Cho, Y.S. / Angove, H. / Brain, C. / Chen, C.H. / Cheng, H. / Cheng, R. / Chopra, R. / Chung, K. / Congreve, M. / Dagostin, C. / Davis, D.J. / Feltell, R. / Giraldes, J. / Hiscock, S.D. / ...Authors: Cho, Y.S. / Angove, H. / Brain, C. / Chen, C.H. / Cheng, H. / Cheng, R. / Chopra, R. / Chung, K. / Congreve, M. / Dagostin, C. / Davis, D.J. / Feltell, R. / Giraldes, J. / Hiscock, S.D. / Kim, S. / Kovats, S. / Lagu, B. / Lewry, K. / Loo, A. / Lu, Y. / Luzzio, M. / Maniara, W. / McMenamin, R. / Mortenson, P.N. / Benning, R. / O'Reilly, M. / Rees, D.C. / Shen, J. / Smith, T. / Wang, Y. / Williams, G. / Woolford, A.J. / Wrona, W. / Xu, M. / Yang, F. / Howard, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4aua.cif.gz | 67.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aua.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 4aua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/4aua ftp://data.pdbj.org/pub/pdb/validation_reports/au/4aua | HTTPS FTP |
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-Related 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: 35019.215 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 1-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q00534, cyclin-dependent kinase |
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#2: Chemical | ChemComp-4AU / |
#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: 2.18 Å3/Da / Density % sol: 43.68 % / Description: NONE |
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Crystal grow | Temperature: 287 K / pH: 5.7 Details: 5MG/ML 0.1 M MES/NAOH PH 5.7,, 4.5% W/V PEG 3350, 25 MM SODIUM NITRATE, 10% V/V GLYCEROL, 10 DEGREES CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9611 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9611 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→71.23 Å / Num. obs: 13277 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.9 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→71.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.961 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.274 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.949 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→71.23 Å
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