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- PDB-3odk: Discovery of cell-active phenyl-imidazole Pin1 inhibitors by stru... -
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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 | ||||||
![]() | ISOMERASE / SBDD / PPIASE / ROTAMASE / SMALL MOLECULE / Proline directed kinase / cell cycle / Oncogenic transformation / Nucleus / Phosphoprotein | ||||||
Function / homology | ![]() cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / positive regulation of GTPase activity / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol 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
Summary document | ![]() | 725.7 KB | Display | ![]() |
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Full document | ![]() | 729.8 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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: 1.5418 Å / Relative weight: 1 |
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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