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- PDB-2x8d: Discovery of a Novel Class of triazolones as Checkpoint Kinase In... -
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Basic information
Entry | Database: PDB / ID: 2x8d | ||||||
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Title | Discovery of a Novel Class of triazolones as Checkpoint Kinase Inhibitors - Hit to Lead Exploration | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK1 | ||||||
![]() | TRANSFERASE / NUCLEOTIDE-BINDING / CYTOSKELETON / PHOSPHOPROTEIN / ISOPEPTIDE BOND / CELL CYCLE / DNA DAMAGE / DNA REPAIR | ||||||
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 / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / replication fork / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / 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 / 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 / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Read, J.A. / Breed, J. / Haye, H. / McCall, E. / Rowsell, S. / Vallentine, A. / White, A. | ||||||
![]() | ![]() Title: Discovery of a Novel Class of Triazolones as Checkpoint Kinase Inhibitors-Hit to Lead Exploration. Authors: Oza, V. / Ashwell, S. / Brassil, P. / Breed, J. / Deng, C. / Ezhuthachan, J. / Haye, H. / Horn, C. / Janetka, J. / Lyne, P. / Newcombe, N. / Otterbien, L. / Pass, M. / Read, J.A. / Roswell, ...Authors: Oza, V. / Ashwell, S. / Brassil, P. / Breed, J. / Deng, C. / Ezhuthachan, J. / Haye, H. / Horn, C. / Janetka, J. / Lyne, P. / Newcombe, N. / Otterbien, L. / Pass, M. / Read, J.A. / Roswell, S. / Su, M. / Toader, D. / Yu, D. / Yu, Y. / Valentine, A. / Webborn, P. / White, A. / Zabludoff, S. / Zheng, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 80.2 KB | Display | ![]() |
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PDB format | ![]() | 58.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x8eC ![]() 2x8iC ![]() 1ia8S 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: 33042.988 Da / Num. of mol.: 1 / Fragment: CHK1KD, RESIDUES 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-X8D / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.8 Details: HANGING DROP. 3UL PLUS 3UL PROTEIN: 7 MG/ML, 25MM TRIS PH7.5, 500MM NACL, 5% GLYCEROL. 5MM DTT WELL: 15-17% (W/V) PEG8000, 250MM AMMONIUM SULPHATE, 2% (V/V) GLYCEROL AND 100 MM SODIUM CACODYLATE PH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 5, 2001 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→37.3 Å / Num. obs: 25219 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / % possible all: 64.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IA8 Resolution: 1.9→37.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.872 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.972 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→37.3 Å
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Refine LS restraints |
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