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Yorodumi- PDB-4nj3: Modulating the interaction between CDK2 and Cyclin A with a Quino... -
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-Basic information
Entry | Database: PDB / ID: 4nj3 | ||||||
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Title | Modulating the interaction between CDK2 and Cyclin A with a Quinoline-based inhibitor | ||||||
Components | Cyclin-dependent kinase 2 | ||||||
Keywords | transferase/transferase inhibitor / CELL CYCLE / INHIBITION / CYCLIN-DEPENDENT KINASE / CANCER / ATP-BINDING / CELL DIVISION / MITOSIS / NUCLEOTIDE-BINDING / PHOSPHORYLATION / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / 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 / FOURIER SYNTHESIS / Resolution: 1.848 Å | ||||||
Authors | Fischmann, T.O. / Hruza, A.W. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Modulating the interaction between CDK2 and cyclin A with a quinoline-based inhibitor. Authors: Deng, Y. / Shipps, G.W. / Zhao, L. / Siddiqui, M.A. / Popovici-Muller, J. / Curran, P.J. / Duca, J.S. / Hruza, A.W. / Fischmann, T.O. / Madison, V.S. / Zhang, R. / McNemar, C.W. / Mayhood, T. ...Authors: Deng, Y. / Shipps, G.W. / Zhao, L. / Siddiqui, M.A. / Popovici-Muller, J. / Curran, P.J. / Duca, J.S. / Hruza, A.W. / Fischmann, T.O. / Madison, V.S. / Zhang, R. / McNemar, C.W. / Mayhood, T.W. / Syto, R. / Annis, A. / Kirschmeier, P. / Lees, E.M. / Parry, D.A. / Windsor, W.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nj3.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nj3.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 4nj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/4nj3 ftp://data.pdbj.org/pub/pdb/validation_reports/nj/4nj3 | 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: 34034.527 Da / Num. of mol.: 1 / Fragment: CDK2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-2KD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 50 MM NA-HEPES, 50 MM, AMMONIUM ACETATE, 8% PEG 4000, 4% GLYCEROL, 1 MM TCEP, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 21, 2003 / Details: mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.848→19 Å / Num. all: 24876 / Num. obs: 23588 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.848→1.87 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.9 / Num. unique all: 435 / % possible all: 70.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.848→19 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.848→19 Å
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