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Yorodumi- PDB-5d1j: CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d1j | ||||||
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Title | CRYSTAL STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2-WT) COMPLEX WITH N-[5-[[[5-(1,1-DIMETHYLETHYL)-2-OXAZOLYL] METHYL]THIO]-2-THIAZOLYL]-4-PIPERIDINECARBOXAMIDE (BMS-387032) | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / KINASE / MITOSIS / CELL CYCLE / TRANSFERASE-TRANSFERASE INHIBIT COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / 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 / 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 / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / response to organic substance / G1/S transition of mitotic cell cycle / 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 / 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 / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / cell division / protein domain specific binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sack, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: N-(Cycloalkylamino)Acyl-2-Aminothiazole Inhibitors Of Cyclin-Dependent Kinase 2. N-[5-[[[5-(1,1-Dimethylethyl) -2-Oxazolyl]Methyl]Thio]-2-Thiazolyl]-4-Piperidinecarboxamide (Bms-387032), A ...Title: N-(Cycloalkylamino)Acyl-2-Aminothiazole Inhibitors Of Cyclin-Dependent Kinase 2. N-[5-[[[5-(1,1-Dimethylethyl) -2-Oxazolyl]Methyl]Thio]-2-Thiazolyl]-4-Piperidinecarboxamide (Bms-387032), A Highly Efficacious And Selective Antitumor Agent Authors: Misra, R.N. / Xiao, H.Y. / Kim, K.S. / Lu, S. / Han, W.C. / Barbosa, S.A. / Hunt, J.T. / Rawlins, D.B. / Shan, W. / Ahmed, S.Z. / Qian, L. / Chen, B.C. / Zhao, R. / Bednarz, M.S. / Kellar, K. ...Authors: Misra, R.N. / Xiao, H.Y. / Kim, K.S. / Lu, S. / Han, W.C. / Barbosa, S.A. / Hunt, J.T. / Rawlins, D.B. / Shan, W. / Ahmed, S.Z. / Qian, L. / Chen, B.C. / Zhao, R. / Bednarz, M.S. / Kellar, K.A. / Mulheron, J.G. / Batorsky, R. / Roongta, U. / Kamath, A. / Marathe, P. / Ranadive, S.A. / Sack, J.S. / Tokarski, J.S. / Pavletich, N.P. / Lee, F.Y.F. / Webster, K.R. / Kimball, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d1j.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d1j.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 5d1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1j ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1j | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-56H / |
#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: 2.09 Å3/Da / Density % sol: 41.06 % |
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Crystal grow | Temperature: 316 K / Method: vapor diffusion, hanging drop Details: 35% poly(ethylene glycol) 5000 monomethyl ester, 0.2 M ammonium acetate, 0.1 M HEPES, pH 7.0, PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 27231 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 28.54 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 39.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.8 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.9214 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.12
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Displacement parameters | Biso mean: 35.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.251 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→23.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.86 Å / Total num. of bins used: 14
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