+Open data
-Basic information
Entry | Database: PDB / ID: 7kjs | ||||||
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Title | Crystal structure of CDK2/cyclin E in complex with PF-06873600 | ||||||
Components |
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Keywords | CELL CYCLE / kinase inhibitor | ||||||
Function / homology | Function and homology information positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation ...positive regulation of mesenchymal stem cell proliferation / homologous chromosome pairing at meiosis / RHOBTB3 ATPase cycle / cyclin-dependent protein serine/threonine kinase regulator activity / G1/S-Specific Transcription / 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 / Association of TriC/CCT with target proteins during biosynthesis / 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 / DNA replication initiation / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / cyclin-dependent kinase / Cajal body / 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 / telomere maintenance / cyclin binding / post-translational protein modification / meiotic cell cycle / positive regulation of DNA replication / response to organic substance / male germ cell nucleus / 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 / Wnt signaling pathway / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / regulation of protein localization / G2/M transition of mitotic cell cycle / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / kinase activity / 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 / regulation of cell cycle / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / 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 / FOURIER SYNTHESIS / Resolution: 2.187 Å | ||||||
Authors | McTigue, M.A. / He, Y. / Ferre, R.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of PF-06873600, a CDK2/4/6 Inhibitor for the Treatment of Cancer. Authors: Freeman-Cook, K.D. / Hoffman, R.L. / Behenna, D.C. / Boras, B. / Carelli, J. / Diehl, W. / Ferre, R.A. / He, Y.A. / Hui, A. / Huang, B. / Huser, N. / Jones, R. / Kephart, S.E. / Lapek, J. / ...Authors: Freeman-Cook, K.D. / Hoffman, R.L. / Behenna, D.C. / Boras, B. / Carelli, J. / Diehl, W. / Ferre, R.A. / He, Y.A. / Hui, A. / Huang, B. / Huser, N. / Jones, R. / Kephart, S.E. / Lapek, J. / McTigue, M. / Miller, N. / Murray, B.W. / Nagata, A. / Nguyen, L. / Niessen, S. / Ninkovic, S. / O'Doherty, I. / Ornelas, M.A. / Solowiej, J. / Sutton, S.C. / Tran, K. / Tseng, E. / Visswanathan, R. / Xu, M. / Zehnder, L. / Zhang, Q. / Zhang, C. / Dann, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kjs.cif.gz | 130.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kjs.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/7kjs ftp://data.pdbj.org/pub/pdb/validation_reports/kj/7kjs | HTTPS FTP |
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-Related structure data
Related structure data | 1w98S 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: 34056.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Protein | Mass: 33848.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCNE1, CCNE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24864 |
#3: Chemical | ChemComp-WG1 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1 M MES pH 6, .18 M magnesium formate, and 9.0 % (w/v) PEG 20000 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.187→100.3 Å / Num. obs: 39969 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.022 / Rrim(I) all: 0.079 / Rsym value: 0.073 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.187→2.3 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5396 / CC1/2: 0.841 / Rpim(I) all: 0.335 / Rrim(I) all: 1.21 / Rsym value: 1.119 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1W98 Resolution: 2.187→83.38 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.209
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Displacement parameters | Biso mean: 61.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.187→83.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.2 Å
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