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Yorodumi- PDB-4a9u: CRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a9u | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CARBOXAMIDE INHIBITOR | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE CHK2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex ...mitotic DNA damage checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / thymocyte apoptotic process / regulation of protein catabolic process / replicative senescence / mitotic spindle assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Stabilization of p53 / protein catabolic process / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / PML body / G2/M transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / Regulation of TP53 Degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / ubiquitin protein ligase binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å | ||||||
Authors | Matijssen, C. / Silva-Santisteban, M.C. / Westwood, I.M. / Siddique, S. / Choi, V. / Sheldrake, P. / van Montfort, R.L.M. / Blagg, J. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2012 Title: Benzimidazole Inhibitors of the Protein Kinase Chk2: Clarification of the Binding Mode by Flexible Side Chain Docking and Protein-Ligand Crystallography Authors: Matijssen, C. / Silva-Santisteban, M.C. / Westwood, I.M. / Siddique, S. / Choi, V. / Sheldrake, P. / Van Montfort, R.L.M. / Blagg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a9u.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a9u.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 4a9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/4a9u ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a9u | HTTPS FTP |
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-Related structure data
Related structure data | 4a9rC 4a9sC 4a9tC 2wtjS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37111.844 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 210-531 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN CDNA LIBRARY / Plasmid: PTHREE-E / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS References: UniProt: O96017, non-specific serine/threonine protein kinase |
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-Non-polymers , 5 types, 100 molecules
#2: Chemical | ChemComp-NO3 / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-A9U / | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | 2-{4-[(1-BENZYLPIPERIDIN-4-YL)METHOXY]PHENYL} -1H-BENZIMIDAZOLE-6-CARBOXAMIDE IS REPRESENTED BY THE ...2-{4-[(1-BENZYLPIPE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.9 % / Description: NONE |
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Crystal grow | Details: 0.1 M HEPES PH 7.5, 0.2 M MAGNESIUM NITRATE, 8-16% (W/V) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→60.26 Å / Num. obs: 12692 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / Biso Wilson estimate: 49.13 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WTJ Resolution: 2.48→40.931 Å / SU ML: 0.75 / σ(F): 0.29 / Phase error: 20.39 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.035 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.48→40.931 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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