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- PDB-8xgv: Optimization Efforts for Identification of Novel Highly Potent Ke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8xgv | ||||||
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Title | Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction (PPI) Inhibitors | ||||||
![]() | Kelch-like ECH-associated protein 1 | ||||||
![]() | PEPTIDE BINDING PROTEIN / chronic kidney disease (CKD) / ![]() | ||||||
Function / homology | ![]() negative regulation of response to oxidative stress / regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otake, K. / Hara, Y. / Ubukata, M. / Inoue, M. / Nagahashi, N. / Motoda, D. / Ogawa, N. / Hantani, Y. / Hantani, R. / Adachi, T. ...Otake, K. / Hara, Y. / Ubukata, M. / Inoue, M. / Nagahashi, N. / Motoda, D. / Ogawa, N. / Hantani, Y. / Hantani, R. / Adachi, T. / Nomura, A. / Yamaguchi, K. / Maekawa, M. / Mamada, H. / Motomura, T. / Sato, M. / Harada, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2 Protein-Protein Interaction Inhibitors. Authors: Otake, K. / Hara, Y. / Ubukata, M. / Inoue, M. / Nagahashi, N. / Motoda, D. / Ogawa, N. / Hantani, Y. / Hantani, R. / Adachi, T. / Nomura, A. / Yamaguchi, K. / Maekawa, M. / Mamada, H. / ...Authors: Otake, K. / Hara, Y. / Ubukata, M. / Inoue, M. / Nagahashi, N. / Motoda, D. / Ogawa, N. / Hantani, Y. / Hantani, R. / Adachi, T. / Nomura, A. / Yamaguchi, K. / Maekawa, M. / Mamada, H. / Motomura, T. / Sato, M. / Harada, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8xgkC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34730.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-A1LVC / ( Mass: 464.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29FN2O4 | ||||
#3: Chemical | ChemComp-ACT / ![]() | ||||
#4: Chemical | ChemComp-SO4 / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.27 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion / pH: 5 Details: The purified Keap1 Kelch domain was concentrated to 6-10 mg/mL and crystallized with the solution containing 0.1 M Na acetate (pH 5.0) and 1.5 M di-ammonium sulfate, and 0-0.15 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.41→55.47 Å / Num. obs: 64842 / % possible obs: 99.1 % / Redundancy: 20.3 % / Biso Wilson estimate: 15.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.017 / Rrim(I) all: 0.079 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.41→1.43 Å / Num. unique obs: 3197 / CC1/2: 0.938 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 21.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→47.18 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.2531157333 Å / Origin y: 61.68946399 Å / Origin z: 38.1455009661 Å
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Refinement TLS group | Selection details: all |