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Yorodumi- PDB-7ovk: Protein kinase MKK7 in complex with 5-bromo-2-hydroxyphenyl-subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ovk | |||||||||
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Title | Protein kinase MKK7 in complex with 5-bromo-2-hydroxyphenyl-substituted pyrazolopyrimidine | |||||||||
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: 2.05 Å | |||||||||
Authors | Kleinboelting, S. / Buehrmann, M. / 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 | 7ovk.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ovk.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ovk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/7ovk ftp://data.pdbj.org/pub/pdb/validation_reports/ov/7ovk | HTTPS FTP |
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-Related structure data
Related structure data | 7oviC 7ovjC 7ovlC 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-GOL / |
#3: Chemical | ChemComp-2I5 / |
#4: 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: 2.45 Å3/Da / Density % sol: 49.74 % |
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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: 0.9999 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 22885 / % possible obs: 100 % / Redundancy: 13.37 % / Biso Wilson estimate: 53.56 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.069 / Net I/σ(I): 19.69 |
Reflection shell | Resolution: 2.05→2.15 Å / Mean I/σ(I) obs: 2.23 / Num. unique obs: 2987 / CC1/2: 0.8 / Rrim(I) all: 1.281 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QFL Resolution: 2.05→45.47 Å / SU ML: 0.282 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.7378 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: 60.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→45.47 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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