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Yorodumi- PDB-2xnb: Discovery and Characterisation of 2-Anilino-4-(thiazol-5-yl) pyri... -
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-Basic information
Entry | Database: PDB / ID: 2xnb | ||||||
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Title | Discovery and Characterisation of 2-Anilino-4-(thiazol-5-yl) pyrimidine Transcriptional CDK Inhibitors as Anticancer Agents | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / CELL CYCLE / CDK9 INHIBITOR | ||||||
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 / telomere maintenance in response to DNA damage / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / cellular response to nitric oxide / 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-dependent protein kinase holoenzyme complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / 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 / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Wang, S. / Griffiths, G. / Midgley, C.A. / Barnett, A.L. / Cooper, M. / Grabarek, J. / Ingram, L. / Jackson, W. / Kontopidis, G. / McClue, S.J. ...Wang, S. / Griffiths, G. / Midgley, C.A. / Barnett, A.L. / Cooper, M. / Grabarek, J. / Ingram, L. / Jackson, W. / Kontopidis, G. / McClue, S.J. / McInnes, C. / McLachlan, J. / Meades, C. / Mezna, M. / Stuart, I. / Thomas, M.P. / Zheleva, D.I. / Lane, D.P. / Jackson, R.C. / Glover, D.M. / Blake, D.G. / Fischer, P.M. | ||||||
Citation | Journal: Chem.Biol. / Year: 2010 Title: Discovery and Characterisation of 2-Anilino-4-(Thiazol-5-Yl)Pyrimidine Transcriptional Cdk Inhibitors as Anticancer Agents Authors: Wang, S. / Griffiths, G. / Midgley, C.A. / Barnett, A.L. / Cooper, M. / Grabarek, J. / Ingram, L. / Jackson, W. / Kontopidis, G. / Mcclue, S.J. / Mcinnes, C. / Mclachlan, J. / Meades, C. / ...Authors: Wang, S. / Griffiths, G. / Midgley, C.A. / Barnett, A.L. / Cooper, M. / Grabarek, J. / Ingram, L. / Jackson, W. / Kontopidis, G. / Mcclue, S.J. / Mcinnes, C. / Mclachlan, J. / Meades, C. / Mezna, M. / Stuart, I. / Thomas, M.P. / Zheleva, D.I. / Lane, D.P. / Jackson, R.C. / Glover, D.M. / Blake, D.G. / Fischer, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xnb.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xnb.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xnb ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xnb | HTTPS FTP |
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-Related structure data
Related structure data | 2xmyC 2clxS C: citing same article (ref.) 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: 33976.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P24941, cyclin-dependent kinase |
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#2: Chemical | ChemComp-Y8L / |
#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: 1.84 Å3/Da / Density % sol: 32.5 % / Description: NONE |
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Crystal grow | pH: 6.8 / Details: 10% PEG 3350, NAF, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 30, 2004 / Details: BLUE MAX-FLUX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→31.88 Å / Num. obs: 25565 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 2.63 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.56 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CLX Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.508 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 340-42 ARE DISORDED. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY 13-18, 147-163.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.293 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→30 Å
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Refine LS restraints |
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