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- PDB-7off: Keap1 kelch domain bound to a small molecule inhibitor of the Kea... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7off | ||||||
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Title | Keap1 kelch domain bound to a small molecule inhibitor of the Keap1-Nrf2 protein-protein interaction | ||||||
![]() | Kelch-like ECH-associated protein 1 | ||||||
![]() | PEPTIDE BINDING PROTEIN / ![]() ![]() ![]() | ||||||
Function / homology | ![]() cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Narayanan, D. / Bach, A. / Gajhede, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Development of Noncovalent Small-Molecule Keap1-Nrf2 Inhibitors by Fragment-Based Drug Discovery. Authors: Narayanan, D. / Tran, K.T. / Pallesen, J.S. / Solbak, S.M.O. / Qin, Y. / Mukminova, E. / Luchini, M. / Vasilyeva, K.O. / Gonzalez Chichon, D. / Goutsiou, G. / Poulsen, C. / Haapanen, N. / ...Authors: Narayanan, D. / Tran, K.T. / Pallesen, J.S. / Solbak, S.M.O. / Qin, Y. / Mukminova, E. / Luchini, M. / Vasilyeva, K.O. / Gonzalez Chichon, D. / Goutsiou, G. / Poulsen, C. / Haapanen, N. / Popowicz, G.M. / Sattler, M. / Olagnier, D. / Gajhede, M. / Bach, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 217.4 KB | Display | ![]() |
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PDB format | ![]() | 146.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7of8C ![]() 7of9C ![]() 7ofaC ![]() 7ofbC ![]() 7ofcC ![]() 7ofdC ![]() 7ofeC ![]() 5fnuS 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
#1: Protein | Mass: 33362.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: Q9Z2X8 | ||||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-DMS / ![]() #4: Chemical | ChemComp-VCB / ( | #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6 and 1.0 M Lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.367→51.59 Å / Num. obs: 71319 / % possible obs: 99.97 % / Redundancy: 17.9 % / Biso Wilson estimate: 14.96 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.09569 / Rpim(I) all: 0.02248 / Rrim(I) all: 0.09834 / Net I/σ(I): 21.56 |
Reflection shell | Resolution: 1.367→1.416 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.328 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 7092 / CC1/2: 0.847 / CC star: 0.958 / Rpim(I) all: 0.4337 / Rrim(I) all: 1.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5FNU Resolution: 1.37→51.59 Å / SU ML: 0.1065 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.6655 / Stereochemistry target values: GeoStd + Monomer Library
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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: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→51.59 Å
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Refine LS restraints |
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LS refinement shell |
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