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- PDB-4dus: Structure of Bace-1 (Beta-Secretase) in complex with N-((2S,3R)-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4dus | ||||||
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Title | Structure of Bace-1 (Beta-Secretase) in complex with N-((2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-((6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl)amino)butan-2-yl)acetamide | ||||||
![]() | Beta-secretase 1![]() | ||||||
![]() | HYDROLASE/Hydrolase Inhibitor / ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sickmier, E.A. | ||||||
![]() | ![]() Title: A Potent and Orally Efficacious, Hydroxyethylamine-Based Inhibitor of beta-Secretase. Authors: Kaller, M.R. / Harried, S.S. / Albrecht, B. / Amarante, P. / Babu-Khan, S. / Bartberger, M.D. / Brown, J. / Brown, R. / Chen, K. / Cheng, Y. / Citron, M. / Croghan, M.D. / Graceffa, R. / ...Authors: Kaller, M.R. / Harried, S.S. / Albrecht, B. / Amarante, P. / Babu-Khan, S. / Bartberger, M.D. / Brown, J. / Brown, R. / Chen, K. / Cheng, Y. / Citron, M. / Croghan, M.D. / Graceffa, R. / Hickman, D. / Judd, T. / Kriemen, C. / La, D. / Li, V. / Lopez, P. / Luo, Y. / Masse, C. / Monenschein, H. / Nguyen, T. / Pennington, L.D. / Miguel, T.S. / Sickmier, E.A. / Wahl, R.C. / Weiss, M.M. / Wen, P.H. / Williamson, T. / Wood, S. / Xue, M. / Yang, B. / Zhang, J. / Patel, V. / Zhong, W. / Hitchcock, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.1 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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: 45822.445 Da / Num. of mol.: 1 / Fragment: UNP residues 43-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-IOD / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-0MP / | #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.05 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 20% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate, 200mM sodium iodide, , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→20 Å / Num. all: 18831 / Num. obs: 18831 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.093 / Χ2: 1.077 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.09 Å2 / Biso mean: 35.9526 Å2 / Biso min: 10.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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