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- PDB-1pxm: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 3-[4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pxm | ||||||
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Title | HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR 3-[4-(2,4-Dimethyl-thiazol-5-yl)-pyrimidin-2-ylamino]-phenol | ||||||
![]() | Cell division protein kinase 2 | ||||||
![]() | TRANSFERASE / PROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / CELL DIVISION / MITOSIS / INHIBITION / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / 3D-STRUCTURE. | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Jackson, W. / Midgley, C. / Griffiths, G. ...Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Jackson, W. / Midgley, C. / Griffiths, G. / McNae, I. / Wu, S.Y. / McInnes, C. / Zheleva, D. / Walkinshaw, M.D. / Fischer, P.M. | ||||||
![]() | ![]() Title: 2-Anilino-4-(thiazol-5-yl)pyrimidine CDK inhibitors: synthesis, SAR analysis, X-ray crystallography, and biological activity. Authors: Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. / Griffiths, G. / Fleming, I. / Green, S. / McNae, I. / Wu, S. ...Authors: Wang, S. / Meades, C. / Wood, G. / Osnowski, A. / Anderson, S. / Yuill, R. / Thomas, M. / Mezna, M. / Jackson, W. / Midgley, C. / Griffiths, G. / Fleming, I. / Green, S. / McNae, I. / Wu, S.Y. / McInnes, C. / Zheleva, D. / Walkinshaw, M.D. / Fischer, P.M. #1: ![]() Title: Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop Authors: Wu, S.Y. / McNae, I. / Kontopidis, G. / McClue, S.J. / McInnes, C. / Stewart, K.J. / Wang, S. / Zheleva, D.I. / Marriage, H. / Lane, D.P. / Taylor, P. / Fischer, P.M. / Walkinshaw, M.D. | ||||||
History |
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Remark 600 | HETEROGEN CK5 500 has alternate conformation with HOH 501,502,503,504,505,506,507,508,and 509. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pxnC ![]() 1pxoC ![]() 1pxpC ![]() 1hclS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() References: UniProt: P24941, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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#2: Chemical | ChemComp-CK5 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 6000, NA-HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→25 Å / Num. all: 9820 / Num. obs: 9784 / % possible obs: 99.9 % / Redundancy: 9.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.53→2.69 Å / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.38 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HCL Resolution: 2.53→25.07 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1203584.05 / Data cutoff high rms absF: 1203584.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.0624 Å2 / ksol: 0.385649 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.53→25.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.53→2.69 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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