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Yorodumi- PDB-3r01: The discovery of novel benzofuran-2-carboxylic acids as potent Pi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r01 | ||||||
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Title | The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors | ||||||
Components | Proto-oncogene serine/threonine-protein kinase pim-1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Pim1 / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / cellular detoxification / regulation of hematopoietic stem cell proliferation / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / ribosomal small subunit binding / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling / Signaling by FLT3 fusion proteins / negative regulation of innate immune response / positive regulation of brown fat cell differentiation / protein serine/threonine kinase activator activity / regulation of transmembrane transporter activity / positive regulation of protein serine/threonine kinase activity / negative regulation of DNA-binding transcription factor activity / cellular response to type II interferon / manganese ion binding / Interleukin-4 and Interleukin-13 signaling / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / cell cycle / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / nucleolus / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Liu, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors. Authors: Xiang, Y. / Hirth, B. / Asmussen, G. / Biemann, H.P. / Bishop, K.A. / Good, A. / Fitzgerald, M. / Gladysheva, T. / Jain, A. / Jancsics, K. / Liu, J. / Metz, M. / Papoulis, A. / Skerlj, R. / ...Authors: Xiang, Y. / Hirth, B. / Asmussen, G. / Biemann, H.P. / Bishop, K.A. / Good, A. / Fitzgerald, M. / Gladysheva, T. / Jain, A. / Jancsics, K. / Liu, J. / Metz, M. / Papoulis, A. / Skerlj, R. / Stepp, J.D. / Wei, R.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r01.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r01.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3r01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/3r01 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r01 | HTTPS FTP |
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-Related 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: 34481.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIM1 / Production host: Escherichia coli (E. coli) References: UniProt: P11309, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-UNE / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.1M imidazole, 1-1.4 M sodium acetate anhydrous, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→84.82 Å / Num. obs: 12957 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→84.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.547 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R Free: 0.323 / 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: 33.814 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→84.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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