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- PDB-4rvk: CHK1 kinase domain with diazacarbazole compound 8: N-[3-(6-cyano-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rvk | ||||||
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Title | CHK1 kinase domain with diazacarbazole compound 8: N-[3-(6-cyano-9H-pyrrolo[2,3-b:5,4-c']dipyridin-3-yl)phenyl]acetamide | ||||||
![]() | Serine/threonine-protein kinase Chk1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / phosphotransfer catalyst / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Activation of ATR in response to replication stress / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / regulation of signal transduction by p53 class mediator / condensed nuclear chromosome / replication fork / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / Signaling by SCF-KIT / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / DNA damage response / chromatin / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wiesmann, C. / Wu, P. | ||||||
![]() | ![]() Title: Mitigation of Acetylcholine Esterase Activity in the 1,7-Diazacarbazole Series of Inhibitors of Checkpoint Kinase 1. Authors: Gazzard, L. / Williams, K. / Chen, H. / Axford, L. / Blackwood, E. / Burton, B. / Chapman, K. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. / Gancia, E. / Gill, M. / ...Authors: Gazzard, L. / Williams, K. / Chen, H. / Axford, L. / Blackwood, E. / Burton, B. / Chapman, K. / Crackett, P. / Drobnick, J. / Ellwood, C. / Epler, J. / Flagella, M. / Gancia, E. / Gill, M. / Goodacre, S. / Halladay, J. / Hewitt, J. / Hunt, H. / Kintz, S. / Lyssikatos, J. / Macleod, C. / Major, S. / Medard, G. / Narukulla, R. / Ramiscal, J. / Schmidt, S. / Seward, E. / Wiesmann, C. / Wu, P. / Yee, S. / Yen, I. / Malek, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 690.8 KB | Display | ![]() |
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Full document | ![]() | 692.4 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 17.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rvlC ![]() 4rvmC ![]() 1zysS C: citing same article ( S: Starting model for refinement |
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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: 34205.199 Da / Num. of mol.: 1 / Fragment: kinase domain, UNP reidues 1-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14757, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-3XK / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: HEPES, isopropanol, PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 7, 2008 |
Radiation | Monochromator: varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→20 Å / Num. all: 29180 / Num. obs: 27108 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.082 / Net I/σ(I): 15.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ZYS Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.882 / SU B: 3.914 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.178 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.424 Å2
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Refine analyze | Luzzati sigma a obs: 0.123 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.888 Å / Total num. of bins used: 25
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