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- PDB-2vtp: Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vtp | ||||||
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Title | Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design. | ||||||
![]() | CELL DIVISION PROTEIN KINASE 2 | ||||||
![]() | TRANSFERASE / MITOSIS / CELL CYCLE / SERINE/THREONINE PROTEIN KINASE | ||||||
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 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cellular response to nitric oxide / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / 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 / Cajal body / cyclin-dependent protein kinase holoenzyme complex / 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 / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / 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 | ![]() ![]() | ||||||
![]() | Wyatt, P.G. / Woodhead, A.J. / Boulstridge, J.A. / Berdini, V. / Carr, M.G. / Cross, D.M. / Danillon, D. / Davis, D.J. / Devine, L.A. / Early, T.R. ...Wyatt, P.G. / Woodhead, A.J. / Boulstridge, J.A. / Berdini, V. / Carr, M.G. / Cross, D.M. / Danillon, D. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Reule, M. / Saxty, G. / Seavers, L.C.A. / Smith, D. / Squires, M.S. / Trewartha, G. / Walker, M.T. / Woolford, A.J. | ||||||
![]() | ![]() Title: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and ...Title: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design. Authors: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / ...Authors: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Reule, M. / Saxty, G. / Seavers, L.C.A. / Smith, D. / Squires, M.S. / Trewartha, G. / Walker, M.T. / Woolford, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.1 KB | Display | ![]() |
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PDB format | ![]() | 59.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vtaC ![]() 2vthC ![]() 2vtiC ![]() 2vtjC ![]() 2vtlC ![]() 2vtmC ![]() 2vtnC ![]() 2vtoC ![]() 2vtqC ![]() 2vtrC ![]() 2vtsC ![]() 2vttC ![]() 2vu3C 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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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.) ![]() ![]() ![]() References: UniProt: P24941, non-specific serine/threonine protein kinase, cyclin-dependent kinase |
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#2: Chemical | ChemComp-LZ9 / {[( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.29 % / Description: NONE |
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Crystal grow | pH: 6.7 Details: 0.1M HEPES/NAOH PH7.0, 0.0475M AMMONIUM ACETATE, 12% W/V PEG3350, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU CCD / Detector: CCD / Details: OSMIC CONFOCAL BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→32.18 Å / Num. obs: 15404 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Biso Wilson estimate: 32.396 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.6 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: IN-HOUSE STRUCTURE Resolution: 2.15→32.12 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 35.36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→32.12 Å
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LS refinement shell | Resolution: 2.15→2.28 Å / Total num. of bins used: 9
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