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- PDB-4l7g: Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclizatio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l7g | ||||||
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Title | Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxy-benzylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against Beta-Secretase-1 (BACE1) | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / Aspartic Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / multivesicular body / hippocampal mossy fiber to CA3 synapse / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / late endosome / synaptic vesicle / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / early endosome / lysosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huestis, M.P. / Liu, W. / Volgraf, M. / Purkey, H. / Wang, W. / Yu, C. / Wu, P. / Smith, D. / Vigers, G. / Dutcher, D. ...Huestis, M.P. / Liu, W. / Volgraf, M. / Purkey, H. / Wang, W. / Yu, C. / Wu, P. / Smith, D. / Vigers, G. / Dutcher, D. / Geck Do, M.K. / Hunt, K.W. / Siu, M. | ||||||
![]() | ![]() Title: Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxycycloalkylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against ...Title: Diethylaminosulfur Trifluoride-Mediated Intramolecular Cyclization of 2-hydroxycycloalkylureas to Fused Bicyclic Aminooxazoline Compounds and Evaluation of Their Biochemical Activity Against β-Secretase-1 (BACE-1) Authors: Huestis, M.P. / Liu, W. / Volgraf, M. / Purkey, H. / Yu, C. / Wang, W. / Smith, D. / Vigers, G. / Dutcher, D. / Hunt, K.W. / Siu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.5 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 | ![]() 4l7hC ![]() 4l7jC ![]() 4lc7C ![]() 1fknS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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: 45603.207 Da / Num. of mol.: 1 / Fragment: UNP residues 57-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-1W0 / ( |
#3: Chemical | ChemComp-DMS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.77 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.9 Details: 12% PEG 3350 and 0.1M NaOAc, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2010 |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. all: 76243 / Num. obs: 75939 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % |
Reflection shell | Resolution: 1.38→1.43 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FKN Resolution: 1.38→16.633 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 18.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.335 Å2 / ksol: 0.442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.38→16.633 Å
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Refine LS restraints |
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LS refinement shell |
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