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Yorodumi- PDB-1h07: CDK2 in complex with a disubstituted 4, 6-bis anilino pyrimidine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h07 | ||||||
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Title | CDK2 in complex with a disubstituted 4, 6-bis anilino pyrimidine CDK4 inhibitor | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / MITOSIS | ||||||
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 / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / 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 / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Beattie, J.F. / Breault, G.A. / Ellston, R.P.A. / Green, S. / Jewsbury, P.J. / Midgley, C.J. / Naven, R.T. / Minshull, C.A. / Pauptit, R.A. / Tucker, J.A. / Pease, J.E. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2003 Title: Cyclin-Dependent Kinase 4 Inhibitors as a Treatment for Cancer. Part 1: Identification and Optimisation of Substituted 4,6-Bis Anilino Pyrimidines Authors: Beattie, J.F. / Breault, G.A. / Ellston, R.P.A. / Green, S. / Jewsbury, P.J. / Midgley, C.J. / Naven, R.T. / Minshull, C.A. / Pauptit, R.A. / Tucker, J.A. / Pease, J.E. #1: Journal: J.Med.Chem. / Year: 1996 Title: High-Resolution Crystal Structures of Human Cyclin-Dependent Kinase 2 with and without ATP: Bound Waters and Natural Ligand as a Guide for Inhibitor Design Authors: Schulze-Gahmen, U. / De Bondt, H. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h07.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h07.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/1h07 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/1h07 | 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: 34002.527 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P24941, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-MFP / (( |
#3: Chemical | ChemComp-MFQ / (( |
#4: 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 Å3/Da / Density % sol: 39 % |
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Crystal grow | pH: 7 Details: PROTEIN AT 10MG/ML WELL BUFFER CONTAINING 17.5% PEG3350, 200MM HEPES, PH7.0, 100MM AMMONIUM ACETATE, pH 7.00 |
Crystal grow | *PLUS Method: unknown / Details: Lawrie, A.M., (1997) Nat.Struct.Biol., 4, 796. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→32.35 Å / Num. obs: 21455 / % possible obs: 88.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 4.7 / % possible all: 71.6 |
Reflection | *PLUS Highest resolution: 1.85 Å / % possible obs: 87.7 % / Num. measured all: 53065 / Rmerge(I) obs: 0.096 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→32.35 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1361929.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 37 - 43 AND 151 - 154 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.3383 Å2 / ksol: 0.383733 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→32.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.96 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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