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Yorodumi- PDB-7f1g: BACE2 xaperone complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f1g | ||||||
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Title | BACE2 xaperone complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-2H,3H-[1,4]dioxino[2,3-c]pyridine-7-carboxamide | ||||||
Components |
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Keywords | HYDROLASE / Beta-secretase 2 | ||||||
Function / homology | Function and homology information memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ueno, T. / Matsuoka, E. / Asada, N. / Yamamoto, S. / Kanegawa, N. / Ito, M. / Ito, H. / Moechars, D. / Rombouts, F.J.R. / Gijsen, H.J.M. / Kusakabe, K.I. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Extremely Selective Fused Pyridine-Derived beta-Site Amyloid Precursor Protein-Cleaving Enzyme (BACE1) Inhibitors with High In Vivo Efficacy through 10s Loop Interactions. Authors: Ueno, T. / Matsuoka, E. / Asada, N. / Yamamoto, S. / Kanegawa, N. / Ito, M. / Ito, H. / Moechars, D. / Rombouts, F.J.R. / Gijsen, H.J.M. / Kusakabe, K.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f1g.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f1g.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 7f1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f1g_validation.pdf.gz | 738.4 KB | Display | wwPDB validaton report |
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Full document | 7f1g_full_validation.pdf.gz | 741.9 KB | Display | |
Data in XML | 7f1g_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 7f1g_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/7f1g ftp://data.pdbj.org/pub/pdb/validation_reports/f1/7f1g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42105.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE2, AEPLC, ALP56, ASP21, CDA13, UNQ418/PRO852 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5Z0, memapsin 1 |
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#2: Protein | Mass: 11968.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-0QQ / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: not available |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→61.17 Å / Num. obs: 77803 / % possible obs: 95.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 14.61 |
Reflection shell | Resolution: 1.5→1.75 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.48 / Num. unique obs: 29017 / % possible all: 96.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.5→61.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.837 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 74.09 Å2 / Biso mean: 27.607 Å2 / Biso min: 10.7 Å2
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Refinement step | Cycle: final / Resolution: 1.5→61.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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