+Open data
-Basic information
Entry | Database: PDB / ID: 4alw | ||||||
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Title | Benzofuropyrimidinone Inhibitors of Pim-1 | ||||||
Components | PIM-1 KINASE | ||||||
Keywords | TRANSFERASE / PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1 | ||||||
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 / positive regulation of brown fat cell differentiation / negative regulation of innate immune response / 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: 1.92 Å | ||||||
Authors | Stout, T.J. / Adams, L. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2012 Title: The Design, Synthesis, and Biological Evaluation of Pim Kinase Inhibitors. Authors: Tsuhako, A.L. / Brown, D.S. / Koltun, E.S. / Aay, N. / Arcalas, A. / Chan, V. / Du, H. / Engst, S. / Franzini, M. / Galan, A. / Huang, P. / Johnston, S. / Kane, B. / Kim, M.H. / Laird, A.D. ...Authors: Tsuhako, A.L. / Brown, D.S. / Koltun, E.S. / Aay, N. / Arcalas, A. / Chan, V. / Du, H. / Engst, S. / Franzini, M. / Galan, A. / Huang, P. / Johnston, S. / Kane, B. / Kim, M.H. / Laird, A.D. / Lin, R. / Mock, L. / Ngan, I. / Pack, M. / Stott, G. / Stout, T.J. / Yu, P. / Zaharia, C. / Zhang, W. / Zhou, P. / Nuss, J.M. / Kearney, P.C. / Xu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4alw.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4alw.ent.gz | 60.3 KB | Display | PDB format |
PDBx/mmJSON format | 4alw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/4alw ftp://data.pdbj.org/pub/pdb/validation_reports/al/4alw | 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: 37557.652 Da / Num. of mol.: 1 / Fragment: PROTEIN KINASE DOMAIN, RESIDUES 406-717 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P11309, EC: 2.7.1.37 | ||||
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#2: Chemical | #3: Chemical | ChemComp-HY7 / | #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: 2.9 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 7.2 / Details: pH 7.2 |
-Data collection
Diffraction | Mean temperature: 155 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→37.42 Å / Num. obs: 33275 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.33 |
Reflection shell | Resolution: 1.92→2.03 Å / Redundancy: 5.92 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.6 / % possible all: 95.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN-HOUSE PIM1 STRUCTURE Resolution: 1.92→37.42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.009 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.118 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.685 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→37.42 Å
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Refine LS restraints |
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