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Yorodumi- PDB-2xpb: DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xpb | ||||||
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Title | DISCOVERY OF CELL-ACTIVE PHENYL-IMIDAZOLE PIN1 INHIBITORS BY STRUCTURE-GUIDED FRAGMENT EVOLUTION | ||||||
Components | PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 1 | ||||||
Keywords | ISOMERASE / PROLINE DIRECTED KINASE / CELL CYCLE / ONCOGENIC TRANSFORMATION | ||||||
Function / homology | Function and homology information 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 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.E. / Richardson, C.M. / Murray, J.B. / Moore, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xpb.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xpb.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 2xpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xpb_validation.pdf.gz | 1010.3 KB | Display | wwPDB validaton report |
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Full document | 2xpb_full_validation.pdf.gz | 1010.8 KB | Display | |
Data in XML | 2xpb_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2xpb_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xpb ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xpb | HTTPS FTP |
-Related structure data
Related structure data | 2xp3C 2xp4C 2xp5C 2xp6C 2xp7C 2xp8C 2xp9C 2xpaC 3odkC 3kceS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18524.525 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13526, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-12P / |
#3: Chemical | ChemComp-4GE / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57 % / Description: NONE |
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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: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 14643 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 2.21 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 2.15 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 97.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KCE Resolution: 2→59.44 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.068 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.174 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.074 Å2
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Refinement step | Cycle: LAST / Resolution: 2→59.44 Å
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