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Open data
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Basic information
Entry | Database: PDB / ID: 3r8v | ||||||
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Title | CDK2 in complex with inhibitor RC-1-135 | ||||||
![]() | Cyclin-dependent kinase 2![]() | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() | ||||||
Function / homology | ![]() cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Betzi, S. / Alam, R. / Han, H. / Becker, A. / Schonbrunn, E. | ||||||
![]() | ![]() Title: Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases. Authors: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / ...Authors: Schonbrunn, E. / Betzi, S. / Alam, R. / Martin, M.P. / Becker, A. / Han, H. / Francis, R. / Chakrasali, R. / Jakkaraj, S. / Kazi, A. / Sebti, S.M. / Cubitt, C.L. / Gebhard, A.W. / Hazlehurst, L.A. / Tash, J.S. / Georg, G.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 | ![]() | 78.3 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qqkC ![]() 3qtqC ![]() 3qtrC ![]() 3qtsC ![]() 3qtuC ![]() 3qtwC ![]() 3qtxC ![]() 3qtzC ![]() 3qu0C ![]() 3qxpC ![]() 3r8uC ![]() 3r8zC ![]() 3r9dC ![]() 3r9hC ![]() 3r9nC ![]() 3r9oC ![]() 3rahC ![]() 3rakC ![]() 3ralC ![]() 3rjcC ![]() 3rk5C ![]() 3rk7C ![]() 3rk9C ![]() 3rkbC ![]() 3rmfC ![]() 3rniC ![]() 3rprC ![]() 3rpvC ![]() 3rpyC ![]() 3rzbC ![]() 3s00C ![]() 3s0oC ![]() 3s1hC ![]() 3sqqC ![]() 4gcjC ![]() 1pw2S C: citing same article ( S: Starting model for refinement |
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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: 34761.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-Z62 / [ |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.21 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5 mg/mL CDK2 protein, 3 mM inhibitor, 15% v/v PEG3350, 50 mM HEPES/NaOH, 50 mM Na/K phosphate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 7, 2008 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→36.14 Å / Num. all: 21860 / Num. obs: 21860 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 53.08 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 13.27 / Num. unique all: 2099 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1PW2 Resolution: 1.9→36.14 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 195443.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.3153 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→36.14 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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