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Open data
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Basic information
Entry | Database: PDB / ID: 7bjx | ||||||
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Title | Crystal structure of CHK1-10pt-mutant complex with compound 26 | ||||||
![]() | Serine/threonine-protein kinase Chk1 | ||||||
![]() | TRANSFERASE / PARKINSON'S DISEASE / LEUCINE-RICH REPEAT KINASE 2 / LRRK2 / CHECKPOINT KINASE 1 / CHK1 / MUTANT / SURROGATE / KINASE INHIBITOR / SBDD | ||||||
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 / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination ...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 / negative regulation of gene expression, epigenetic / regulation of double-strand break repair via homologous recombination / 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 / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / positive regulation of cell cycle / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. / Surgenor, A.E. / Williamson, D.S. | ||||||
![]() | ![]() Title: Design and Synthesis of Pyrrolo[2,3- d ]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate. Authors: Williamson, D.S. / Smith, G.P. / Mikkelsen, G.K. / Jensen, T. / Acheson-Dossang, P. / Badolo, L. / Bedford, S.T. / Chell, V. / Chen, I.J. / Dokurno, P. / Hentzer, M. / Newland, S. / Ray, S.C. ...Authors: Williamson, D.S. / Smith, G.P. / Mikkelsen, G.K. / Jensen, T. / Acheson-Dossang, P. / Badolo, L. / Bedford, S.T. / Chell, V. / Chen, I.J. / Dokurno, P. / Hentzer, M. / Newland, S. / Ray, S.C. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Christensen, K.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119.3 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 450.1 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bjdC ![]() 7bjeC ![]() 7bjhC ![]() 7bjjC ![]() 7bjmC ![]() 7bjoC ![]() 7bjrC ![]() 7bk1C ![]() 7bk2C ![]() 7bk3C ![]() 7bknC ![]() 7bkoC ![]() 5oopS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34094.207 Da / Num. of mol.: 2 Mutation: N59L, V68I, L84M, Y86L, C87A, E91S, E134H, S147A, F149Y, G150S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14757, non-specific serine/threonine protein kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→28.3 Å / Num. obs: 31723 / % possible obs: 95.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.18→2.24 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2 / Num. unique obs: 2356 / % possible all: 96.5 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5oop Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.56 / SU ML: 0.193 / SU R Cruickshank DPI: 0.4213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 190.32 Å2 / Biso mean: 57.43 Å2 / Biso min: 22.9 Å2
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Refinement step | Cycle: final / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.528 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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