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Yorodumi- PDB-2vtm: Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vtm | ||||||
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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. | ||||||
Components | CELL DIVISION PROTEIN KINASE 2 | ||||||
Keywords | TRANSFERASE / MITOSIS / CELL CYCLE / SERINE/THREONINE PROTEIN KINASE | ||||||
Function / homology | Function and homology information Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich ...Replication initiator protein RctB, central region / RctB, helix turn helix domain / Vibrionales, replication initiator protein RctB, central region / RctB helix turn helix domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vtm.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vtm.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vtm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vtm_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 2vtm_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 2vtm_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2vtm_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/2vtm ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vtm | HTTPS FTP |
-Related structure data
Related structure data | 2vtaC 2vthC 2vtiC 2vtjC 2vtlC 2vtnC 2vtoC 2vtpC 2vtqC 2vtrC 2vtsC 2vttC 2vu3C C: citing same article (ref.) |
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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, non-specific serine/threonine protein kinase, cyclin-dependent kinase |
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#2: Chemical | ChemComp-LZM / |
#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: 1.97 Å3/Da / Density % sol: 36.94 % / 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: ROTATING ANODE / Type: RIGAKU RU200HR / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Details: OSMIC CONFOCAL PURPLE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→42.89 Å / Num. obs: 13133 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 37.66 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.25→2.33 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.8 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE STRUCTURE Resolution: 2.25→42.89 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 37.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→42.89 Å
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LS refinement shell | Resolution: 2.25→2.39 Å / Total num. of bins used: 9
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