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Yorodumi- PDB-3orn: Mitogen-activated protein kinase kinase 1 (MEK1) in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 3orn | ||||||
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Title | Mitogen-activated protein kinase kinase 1 (MEK1) in complex with CH4987655 and MgAMP-PNP | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / kinase / kinase inhibitor / allosteric / mitogen-activated protein kinase kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants / regulation of Golgi inheritance / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / protein kinase activator activity / ERBB2-ERBB3 signaling pathway / endodermal cell differentiation / face development / MAPK3 (ERK1) activation / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / Schwann cell development / keratinocyte differentiation / ERK1 and ERK2 cascade / myelination / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / cell motility / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / neuron differentiation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome / heart development / scaffold protein binding / protein tyrosine kinase activity / positive regulation of ERK1 and ERK2 cascade / early endosome / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Lukacs, C.M. / Janson, C. / Schuck, V. / Belunis, C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2011 Title: Design and synthesis of novel allosteric MEK inhibitor CH4987655 as an orally available anticancer agent. Authors: Isshiki, Y. / Kohchi, Y. / Iikura, H. / Matsubara, Y. / Asoh, K. / Murata, T. / Kohchi, M. / Mizuguchi, E. / Tsujii, S. / Hattori, K. / Miura, T. / Yoshimura, Y. / Aida, S. / Miwa, M. / ...Authors: Isshiki, Y. / Kohchi, Y. / Iikura, H. / Matsubara, Y. / Asoh, K. / Murata, T. / Kohchi, M. / Mizuguchi, E. / Tsujii, S. / Hattori, K. / Miura, T. / Yoshimura, Y. / Aida, S. / Miwa, M. / Saitoh, R. / Murao, N. / Okabe, H. / Belunis, C. / Janson, C. / Lukacs, C. / Schuck, V. / Shimma, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3orn.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3orn.ent.gz | 53.8 KB | Display | PDB format |
PDBx/mmJSON format | 3orn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/3orn ftp://data.pdbj.org/pub/pdb/validation_reports/or/3orn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34239.438 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 62-270, 303-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Escherichia coli (E. coli) References: UniProt: Q02750, mitogen-activated protein kinase kinase |
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-Non-polymers , 6 types, 49 molecules
#2: Chemical | ChemComp-ANP / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-3OR / | ||
#5: Chemical | ChemComp-PGE / | ||
#6: Chemical | ChemComp-SO4 / #7: 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: 4.8 Å3/Da / Density % sol: 74.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2M Ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→42.44 Å / Num. all: 16367 / Num. obs: 16356 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 81.1 Å2 / Rsym value: 0.168 / Net I/σ(I): 1.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2367 / Rsym value: 0.447 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→39.45 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 919200.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.1171 Å2 / ksol: 0.360087 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→39.45 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.92 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
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Xplor file |
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