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- PDB-5opb: Structure of CHK1 10-pt. mutant complex with indazole LRRK2 inhibitor -
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Open data
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Basic information
Entry | Database: PDB / ID: 5opb | ||||||
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Title | Structure of CHK1 10-pt. mutant complex with indazole LRRK2 inhibitor | ||||||
![]() | Serine/threonine-protein kinase Chk1 | ||||||
![]() | TRANSFERASE / Parkinson's disease / Leucine-rich repeat kinase 2 / LRRK2 / Checkpoint kinase 1 / CHK1 / mutant / surrogate / kinase inhibitor | ||||||
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. / Williamson, D.S. / Acheson-Dossang, P. / Chen, I. / Murray, J.B. / Shaw, T. / Surgenor, A.E. | ||||||
![]() | ![]() Title: Design of Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Crystallographic Surrogate Derived from Checkpoint Kinase 1 (CHK1). Authors: Williamson, D.S. / Smith, G.P. / Acheson-Dossang, P. / Bedford, S.T. / Chell, V. / Chen, I.J. / Daechsel, J.C.A. / Daniels, Z. / David, L. / Dokurno, P. / Hentzer, M. / Herzig, M.C. / ...Authors: Williamson, D.S. / Smith, G.P. / Acheson-Dossang, P. / Bedford, S.T. / Chell, V. / Chen, I.J. / Daechsel, J.C.A. / Daniels, Z. / David, L. / Dokurno, P. / Hentzer, M. / Herzig, M.C. / Hubbard, R.E. / Moore, J.D. / Murray, J.B. / Newland, S. / Ray, S.C. / Shaw, T. / Surgenor, A.E. / Terry, L. / Thirstrup, K. / 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 | ![]() | 75.6 KB | Display | ![]() |
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PDB format | ![]() | 54 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.7 KB | Display | ![]() |
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Full document | ![]() | 736.3 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oopSC ![]() 5oorC ![]() 5ootC ![]() 5op2C ![]() 5op4C ![]() 5op5C ![]() 5op7C ![]() 5oprC ![]() 5opsC ![]() 5opuC ![]() 5opvC ![]() 5oq5C ![]() 5oq6C ![]() 5oq7C ![]() 5oq8C 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: 34094.207 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-A1N / ( | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.72 % |
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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 | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.51→41.83 Å / Num. obs: 44891 / % possible obs: 90.6 % / Redundancy: 2.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.025 / Rrim(I) all: 0.042 / Net I/σ(I): 15.5 / Num. measured all: 113306 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OOP Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.638 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.43 Å2 / Biso mean: 32.468 Å2 / Biso min: 13.09 Å2
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Refinement step | Cycle: final / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.633 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
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