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Open data
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Basic information
Entry | Database: PDB / ID: 7xlp | ||||||
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Title | MEK1 bound to DS03090629 | ||||||
![]() | Dual specificity mitogen-activated protein kinase kinase 1 | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kishikawa, S. / Takano, K. / Ubukata, O. / Hanzawa, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Discovery of a Novel ATP-Competitive MEK Inhibitor DS03090629 that Overcomes Resistance Conferred by BRAF Overexpression in BRAF-Mutated Melanoma. Authors: Takano, K. / Munehira, Y. / Hatanaka, M. / Murakami, R. / Shibata, Y. / Shida, T. / Takeuchi, K. / Takechi, S. / Tabata, T. / Shimada, T. / Kishikawa, S. / Matsui, Y. / Ubukata, O. / Seki, T. / Kaneta, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.8 KB | Display | ![]() |
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PDB format | ![]() | 106.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xncC ![]() 5bx0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38916.879 Da / Num. of mol.: 1 / Mutation: S298N, S299K, Y300K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q02750, ![]() | ||||
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#2: Chemical | ChemComp-FZC / ( | ||||
#3: Chemical | ChemComp-DMS / ![]() | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 100 mM Tris (pH 7.75), 200 mM calcium chloride, 2% DMSO, 18-20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→49.5 Å / Num. obs: 23655 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 43.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.327 / Rpim(I) all: 0.079 / Rrim(I) all: 0.337 / Net I/σ(I): 9.2 / Num. measured all: 436693 / Scaling rejects: 1873 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5BX0 Resolution: 2.1→49.5 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.6 Å2 / Biso mean: 63.2445 Å2 / Biso min: 33.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→49.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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