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- PDB-7chn: Crystal structure of TTK kinase domain in complex with compound 9 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7chn | ||||||
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Title | Crystal structure of TTK kinase domain in complex with compound 9 | ||||||
![]() | Dual specificity protein kinase TTK | ||||||
![]() | TRANSFERASE / Kinase MPS1 TTK Structure-guided drug design | ||||||
Function / homology | ![]() protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization ...protein localization to meiotic spindle midzone / meiotic spindle assembly checkpoint signaling / kinetochore binding / female meiosis chromosome segregation / protein localization to kinetochore / dual-specificity kinase / spindle organization / mitotic spindle assembly checkpoint signaling / protein serine/threonine/tyrosine kinase activity / mitotic spindle organization / chromosome segregation / kinetochore / spindle / protein tyrosine kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / ATP binding / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, H.L. / Cho, H.Y. / Park, Y.W. / Lee, Y.H. / Son, J.B. / Ko, E.H. / Choi, H.G. / Kim, N.D. | ||||||
![]() | ![]() Title: X-ray Crystal Structure-Guided Design and Optimization of 7 H -Pyrrolo[2,3- d ]pyrimidine-5-carbonitrile Scaffold as a Potent and Orally Active Monopolar Spindle 1 Inhibitor. Authors: Lee, Y. / Kim, H. / Kim, H. / Cho, H.Y. / Jee, J.G. / Seo, K.A. / Son, J.B. / Ko, E. / Choi, H.G. / Kim, N.D. / Kim, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 87.3 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7chmC ![]() 7chtC ![]() 7cilC ![]() 7cjaC ![]() 7clhC ![]() 6b4wS 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: 32892.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FZL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: 7-9% PEG 10000 0.08-0.14 M magnesium acetate 0.1 M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 17566 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.33 Å2 / CC1/2: 1 / Net I/σ(I): 39.958 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.668 / Num. unique obs: 844 / CC1/2: 0.911 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6B4W Resolution: 2.4→41.02 Å / SU ML: 0.2903 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.753 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→41.02 Å
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Refine LS restraints |
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LS refinement shell |
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