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Yorodumi- PDB-6ayd: Pim1 complexed with N-(6-(4-hydroxyphenyl)-1H-indazol-3-yl)cyclop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ayd | ||||||
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Title | Pim1 complexed with N-(6-(4-hydroxyphenyl)-1H-indazol-3-yl)cyclopropanecarboxamide | ||||||
Components | Serine/threonine-protein kinase pim-1 | ||||||
Keywords | Transferase/Transferase Inhibitor / Kinase / Transferase-Transferase Inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / positive regulation of cardiac muscle cell proliferation / positive regulation of TORC1 signaling ...positive regulation of cardioblast proliferation / regulation of hematopoietic stem cell proliferation / cellular detoxification / vitamin D receptor signaling pathway / STAT5 activation downstream of FLT3 ITD mutants / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal small subunit binding / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Shewchuk, L.M. / Henley, Z.A. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2017 Title: From PIM1 to PI3K delta via GSK3 beta : Target Hopping through the Kinome. Authors: Henley, Z.A. / Bax, B.D. / Inglesby, L.M. / Champigny, A. / Gaines, S. / Faulder, P. / Le, J. / Thomas, D.A. / Washio, Y. / Baldwin, I.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ayd.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ayd.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ayd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ayd_validation.pdf.gz | 666.7 KB | Display | wwPDB validaton report |
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Full document | 6ayd_full_validation.pdf.gz | 666.9 KB | Display | |
Data in XML | 6ayd_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6ayd_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/6ayd ftp://data.pdbj.org/pub/pdb/validation_reports/ay/6ayd | HTTPS FTP |
-Related structure data
Related structure data | 5oy4C 2bikS S: Starting model for refinement C: citing same article (ref.) |
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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: 38062.148 Da / Num. of mol.: 1 / Fragment: UNP residues 1-312 / Mutation: R250G 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 | ChemComp-C2J / |
#3: 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: 2.88 Å3/Da / Density % sol: 57.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 1M succinate pH 7.0, 0.1M BisTrisPropane, 1% 1,6-hexanediol |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 7834 / % possible obs: 94 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15 |
Reflection shell | Resolution: 3→3.078 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 385 / % possible all: 63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BIK Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.885 / SU B: 36.658 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.48 Å2 / Biso mean: 73.88 Å2 / Biso min: 23.83 Å2
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Refinement step | Cycle: final / Resolution: 3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.681 Å / Origin y: -40.228 Å / Origin z: -0.63 Å
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