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- PDB-2cgv: Identification of chemically diverse Chk1 inhibitors by receptor-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2cgv | ||||||
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Title | Identification of chemically diverse Chk1 inhibitors by receptor- based virtual screening | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK1 | ||||||
![]() | TRANSFERASE / DOCKING / DRUG DESIGN / ONCOLOGY / VIRTUAL SCREENING / ATP- BINDING / CELL CYCLE / DNA DAMAGE / DNA REPAIR / KINASE / NUCLEAR PROTEIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION / POLYMORPHISM / SERINE/THREONINE-PROTEIN KINASE / UBL CONJUGATION | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Foloppe, N. / Fisher, L.M. / Howes, R. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E. | ||||||
![]() | ![]() Title: Identification of Chemically Diverse Chk1 Inhibitors by Receptor-Based Virtual Screening. Authors: Foloppe, N. / Fisher, L.M. / Howes, R. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.1 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cguC ![]() 2cgwC ![]() 2cgxC ![]() 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: 34148.148 Da / Num. of mol.: 1 / Fragment: N-TERMINAL KINASE DOMAIN, RESIDUES 1-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-3B3 / ( |
#3: Water | ChemComp-HOH / |
Compound details | REQUIRED FOR CHECKPOINT MEDIATED CELL CYCLE ARREST IN RESPONSE TO DNA DAMAGE OR THE PRESENCE OF ...REQUIRED FOR CHECKPOINT |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 10278 / % possible obs: 79.9 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.2 / % possible all: 36 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IA8 Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.872 / SU B: 12.006 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 47.47 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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