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- PDB-2ycf: Crystal Structure of Checkpoint Kinase 2 in complex with Inhibito... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ycf | ||||||
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Title | Crystal Structure of Checkpoint Kinase 2 in complex with Inhibitor PV1531 | ||||||
![]() | SERINE/THREONINE-PROTEIN KINASE CHK2 | ||||||
![]() | TRANSFERASE / ANTICANCER / ANTICANCER DRUG DESIGN | ||||||
Function / homology | ![]() mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / 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 ...mitotic DNA damage checkpoint signaling / regulation of autophagosome assembly / 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 / PML body / cellular response to gamma radiation / intrinsic apoptotic signaling pathway in response to DNA damage / G2/M transition of mitotic cell cycle / 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 / ubiquitin protein ligase binding / DNA damage response / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lountos, G.T. / Jobson, A.G. / Tropea, J.E. / Self, C.R. / Pommier, Y. / Shoemaker, R.H. / Zhang, G. / Waugh, D.S. | ||||||
![]() | ![]() Title: Structural Characterization of Inhibitor Complexes with Checkpoint Kinase 2 (Chk2), a Drug Target for Cancer Therapy. Authors: Lountos, G.T. / Jobson, A.G. / Tropea, J.E. / Self, C.R. / Zhang, G. / Pommier, Y. / Shoemaker, R.H. / Waugh, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.4 KB | Display | ![]() |
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PDB format | ![]() | 106.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xk9C ![]() 2ycqC ![]() 2ycrC ![]() 2ycsC ![]() 2cn5S 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36433.125 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 210-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O96017, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-YCF / ( |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NO3 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.3 % / Description: NONE |
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Crystal grow | pH: 7.8 Details: 0.1M HEPES PH 7.8, 0.1 M MAGNESIUM NITRATE, 14% W/V PEG 3350, 16% V/V ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-300 / Detector: CCD / Date: Jun 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 44051 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 48.3 |
Reflection shell | Resolution: 1.77→1.82 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CN5 Resolution: 1.77→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.511 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→50 Å
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Refine LS restraints |
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