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Yorodumi- PDB-4hyh: X-RAY Crystal structure of compound 39 bound to human chk1 kinase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hyh | ||||||
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Title | X-RAY Crystal structure of compound 39 bound to human chk1 kinase domain | ||||||
Components | Serine/threonine-protein kinase Chk1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SERINE/THREONINE-PROTEIN KINASE CHK1 INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / nucleus organization ...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 / nucleus organization / negative regulation of gene expression, epigenetic / 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 / positive regulation of cell cycle / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of ATR in response to replication stress / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / condensed nuclear chromosome / replication fork / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Signaling by SCF-KIT / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / G2/M transition of mitotic cell cycle / regulation of cell population proliferation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / DNA replication / non-specific serine/threonine protein kinase / protein kinase activity / chromatin remodeling / protein phosphorylation / protein domain specific binding / intracellular membrane-bounded organelle / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Fischmann, T.O. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Structure-based design and optimization of 2-aminothiazole-4-carboxamide as a new class of CHK1 inhibitors. Authors: Huang, X. / Cheng, C.C. / Fischmann, T.O. / Duca, J.S. / Richards, M. / Tadikonda, P.K. / Reddy, P.A. / Zhao, L. / Arshad Siddiqui, M. / Parry, D. / Davis, N. / Seghezzi, W. / Wiswell, D. / Shipps, G.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hyh.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hyh.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hyh_validation.pdf.gz | 696 KB | Display | wwPDB validaton report |
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Full document | 4hyh_full_validation.pdf.gz | 702 KB | Display | |
Data in XML | 4hyh_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 4hyh_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/4hyh ftp://data.pdbj.org/pub/pdb/validation_reports/hy/4hyh | HTTPS FTP |
-Related 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: 33042.988 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 1-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHEK1, CHK1 / Cell line (production host): SF22 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O14757, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-1AM / |
#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: 2.39 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-Cl pH 7.5 1% v/v n-butanol 2.5% v/v DMSO 25% v/v Glycerol 6 to 12% PEG 3.25K 2.5 mM TCEP-Cl 10 mM Na2-Dithionite, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2007 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24 Å / Num. obs: 33958 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1696 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→24 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→24 Å
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