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- PDB-1ke6: CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH N-METHYL-{4-[2-(7... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ke6 | ||||||
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Title | CYCLIN-DEPENDENT KINASE 2 (CDK2) COMPLEXED WITH N-METHYL-{4-[2-(7-OXO-6,7-DIHYDRO-8H-[1,3]THIAZOLO[5,4-E]INDOL-8-YLIDENE)HYDRAZINO]PHENYL}METHANESULFONAMIDE | ||||||
![]() | Cell division protein kinase 2 | ||||||
![]() | TRANSFERASE / cyclin / kinase | ||||||
Function / homology | ![]() cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cellular response to nitric oxide / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / : / cyclin binding / post-translational protein modification / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / DNA replication / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe, R.T. / Hassell, A.H. / Shewchuk, L.M. / Kuyper, L.F. | ||||||
![]() | ![]() Title: Oxindole-based inhibitors of cyclin-dependent kinase 2 (CDK2): design, synthesis, enzymatic activities, and X-ray crystallographic analysis. Authors: Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Harris, P.A. / Hassell, A. / Holmes, W.D. / Hunter, R.N. / Lackey, K.E. / Lovejoy, ...Authors: Bramson, H.N. / Corona, J. / Davis, S.T. / Dickerson, S.H. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Harris, P.A. / Hassell, A. / Holmes, W.D. / Hunter, R.N. / Lackey, K.E. / Lovejoy, B. / Luzzio, M.J. / Montana, V. / Rocque, W.J. / Rusnak, D. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ke5C ![]() 1ke7C ![]() 1ke8C ![]() 1ke9C ![]() 1hckS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-LS2 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG3340, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Shewchuk L., (2000) J. Med. Chem., 43, 133. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 23, 1998 / Details: mirrors |
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→18 Å / Num. all: 20278 / Num. obs: 19650 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 11.5 / Num. unique all: 1871 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 500 Å / Num. obs: 19650 / % possible obs: 96.9 % / Num. measured all: 98375 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Rmerge(I) obs: 0.211 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HCK Resolution: 2→18 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.11 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Rfactor Rfree error: 0.014
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Refinement | *PLUS Rfactor obs: 0.191 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.191 / Lowest resolution: 18 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Rfactor Rfree: 0.242 / Rfactor Rwork: 0.199 |