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Yorodumi- PDB-2cgw: Identification of chemically diverse Chk1 inhibitors by receptor-... -
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-Basic information
Entry | Database: PDB / ID: 2cgw | ||||||
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Title | Identification of chemically diverse Chk1 inhibitors by receptor- based virtual screening | ||||||
Components | SERINE/THREONINE-PROTEIN KINASE CHK1 | ||||||
Keywords | 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 | 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 / Activation of ATR in response to replication stress / inner cell mass cell proliferation / 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 / Activation of ATR in response to replication stress / 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 / condensed nuclear chromosome / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / 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 / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M transition of mitotic cell cycle / Processing of DNA double-strand break ends / regulation of cell population proliferation / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromatin remodeling / non-specific serine/threonine protein kinase / protein kinase activity / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Foloppe, N. / Fisher, L.M. / Howes, R. / Potter, A. / Robertson, A.G.S. / Surgenor, A.E. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2006 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cgw.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cgw.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 2cgw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cgw_validation.pdf.gz | 731.2 KB | Display | wwPDB validaton report |
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Full document | 2cgw_full_validation.pdf.gz | 738.3 KB | Display | |
Data in XML | 2cgw_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 2cgw_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/2cgw ftp://data.pdbj.org/pub/pdb/validation_reports/cg/2cgw | HTTPS FTP |
-Related structure data
Related structure data | 2cguC 2cgvC 2cgxC 1ia8S S: Starting model for refinement C: citing same article (ref.) |
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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
#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.) HOMO SAPIENS (human) / Plasmid: PFASTBAC1/CHK1 1-289 C8H / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O14757, EC: 2.7.1.37 |
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#2: Chemical | ChemComp-3C3 / |
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 |
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: 2.2→30 Å / Num. obs: 17692 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.2→2.31 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.9 / % possible all: 79.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IA8 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.574 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.224 / 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: 37.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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