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Open data
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Basic information
Entry | Database: PDB / ID: 6cje | ||||||
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Title | Crystal Structure of Mnk2-D228G in complex with Inhibitor | ||||||
![]() | MAP kinase-interacting serine/threonine-protein kinase 2 | ||||||
![]() | Transferase/Transferase Inhibitor / Transferase-Transferase Inhibitor complex / mnk1 inhibitor | ||||||
Function / homology | ![]() calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calcium/calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding ...calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calcium/calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Q. | ||||||
![]() | ![]() Title: Structure-based Design of Pyridone-Aminal eFT508 Targeting Dysregulated Translation by Selective Mitogen-activated Protein Kinase Interacting Kinases 1 and 2 (MNK1/2) Inhibition. Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. ...Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. / Jessen, K.A. / Molter, J. / Murphy, D. / Neal, M. / Parker, G.S. / Shaghafi, M. / Sperry, S. / Staunton, J. / Stumpf, C.R. / Thompson, P.A. / Tran, C. / Webber, S.E. / Wegerski, C.J. / Zheng, H. / Webster, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
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PDB format | ![]() | 51.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6cj5C ![]() 6cjhC ![]() 6cjwC ![]() 6cjyC ![]() 6ck3C ![]() 6ck6C ![]() 6ckiC ![]() 2hw7S C: citing same article ( S: Starting model for refinement |
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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: 35604.461 Da / Num. of mol.: 1 / Mutation: D228G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9HBH9, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-F4A / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.78 % |
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Crystal grow | Temperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20-30% (w/v) polyacrylic acid 5100, 1-5% PEG 400, and 50 mM Hepes (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→40 Å / Num. obs: 6977 / % possible obs: 98 % / Redundancy: 10.1 % / Net I/σ(I): 4 |
Reflection shell | Resolution: 3.35→3.44 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2hw7 Resolution: 3.36→38.78 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.83 / SU B: 31.078 / SU ML: 0.488 / Cross valid method: THROUGHOUT / ESU R Free: 0.62 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.356 Å2
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Refinement step | Cycle: 1 / Resolution: 3.36→38.78 Å
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Refine LS restraints |
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