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- PDB-3odk: Discovery of cell-active phenyl-imidazole Pin1 inhibitors by stru... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3odk | ||||||
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Title | Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Potter, A. / Oldfield, V. / Nunns, C. / Fromont, C. / Ray, S. / Northfield, C.J. / Bryant, C.J. / Scrace, S.F. / Robinson, D. / Matossova, N. ...Potter, A. / Oldfield, V. / Nunns, C. / Fromont, C. / Ray, S. / Northfield, C.J. / Bryant, C.J. / Scrace, S.F. / Robinson, D. / Matossova, N. / Baker, L. / Dokurno, P. / Surgenor, A.E. / Davis, B.E. / Richardson, C.M. / Murray, J.B. / Moore, J.D. | ||||||
![]() | ![]() Title: Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution. Authors: Potter, A. / Oldfield, V. / Nunns, C. / Fromont, C. / Ray, S. / Northfield, C.J. / Bryant, C.J. / Scrace, S.F. / Robinson, D. / Matossova, N. / Baker, L. / Dokurno, P. / Surgenor, A.E. / ...Authors: Potter, A. / Oldfield, V. / Nunns, C. / Fromont, C. / Ray, S. / Northfield, C.J. / Bryant, C.J. / Scrace, S.F. / Robinson, D. / Matossova, N. / Baker, L. / Dokurno, P. / Surgenor, A.E. / Davis, B. / Richardson, C.M. / Murray, J.B. / Moore, J.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.6 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xp3C ![]() 2xp4C ![]() 2xp5C ![]() 2xp6C ![]() 2xp7C ![]() 2xp8C ![]() 2xp9C ![]() 2xpaC ![]() 2xpbC 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: 18524.525 Da / Num. of mol.: 1 / Mutation: R14A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PE4 / ![]() |
#3: Chemical | ChemComp-ODK / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.2M Ammonium sulphate, 0.1M HEPES buffer, 1% PEG 400, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.3→58.93 Å / Num. all: 14924 / Num. obs: 9853 / % possible obs: 69.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.17 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 1.19 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 1.2 / % possible all: 68.5 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→58.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.36 Å / Total num. of bins used: 20
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