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Yorodumi- PDB-7ovl: Protein kinase MKK7 in complex with methoxycyclohexyl-substituted... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ovl | ||||||
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Title | Protein kinase MKK7 in complex with methoxycyclohexyl-substituted indazole | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 7 | ||||||
Keywords | TRANSFERASE / Inhibitor / Complex / MKK7 / Kinase / Triazole / Click-Chemistry / CuACC | ||||||
Function / homology | Function and homology information JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / : / positive regulation of telomere capping / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / Uptake and function of anthrax toxins / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / : / positive regulation of telomere capping / Fc-epsilon receptor signaling pathway / MAP kinase kinase activity / Uptake and function of anthrax toxins / cellular response to interleukin-1 / MAP kinase activity / response to tumor necrosis factor / response to UV / stress-activated MAPK cascade / JNK cascade / positive regulation of JUN kinase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / cellular response to lipopolysaccharide / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / positive regulation of ERK1 and ERK2 cascade / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Buehrmann, M. / Wiese, J.N. / Mueller, M.P. / Rauh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 Title: Optimization of Covalent MKK7 Inhibitors via Crude Nanomole-Scale Libraries. Authors: Gehrtz, P. / Marom, S. / Buhrmann, M. / Hardick, J. / Kleinbolting, S. / Shraga, A. / Dubiella, C. / Gabizon, R. / Wiese, J.N. / Muller, M.P. / Cohen, G. / Babaev, I. / Shurrush, K. / Avram, ...Authors: Gehrtz, P. / Marom, S. / Buhrmann, M. / Hardick, J. / Kleinbolting, S. / Shraga, A. / Dubiella, C. / Gabizon, R. / Wiese, J.N. / Muller, M.P. / Cohen, G. / Babaev, I. / Shurrush, K. / Avram, L. / Resnick, E. / Barr, H. / Rauh, D. / London, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ovl.cif.gz | 150.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ovl.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ovl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/7ovl ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ovl | HTTPS FTP |
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-Related structure data
Related structure data | 7oviC 7ovjC 7ovkC 7ovmC 7ovnC 6qflS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36146.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Production host: Escherichia coli (E. coli) References: UniProt: O14733, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-1XZ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 180-220 mM sodium citrate, 15-25 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9197 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9197 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 8090 / % possible obs: 100 % / Redundancy: 12.99 % / Biso Wilson estimate: 91.18 Å2 / Rrim(I) all: 0.112 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 1.57 / Num. unique obs: 766 / CC1/2: 0.76 / Rrim(I) all: 1.511 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QFL Resolution: 2.9→49.09 Å / SU ML: 0.4832 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4197 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→49.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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