+
Open data
-
Basic information
Entry | Database: PDB / ID: 6uvp | ||||||
---|---|---|---|---|---|---|---|
Title | BACE-1 in complex with compound #3 | ||||||
![]() | Beta-secretase 1 | ||||||
![]() | HYDROLASE/INHIBITOR / protease / inhibitor / complex / 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 / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / 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 | ![]() ![]() ![]() | ||||||
![]() | Hendle, J. / Timm, D.E. | ||||||
![]() | ![]() Title: Preparation and biological evaluation of BACE1 inhibitors: Leveraging trans-cyclopropyl moieties as ligand efficient conformational constraints. Authors: Winneroski, L.L. / Erickson, J.A. / Green, S.J. / Lopez, J.E. / Stout, S.L. / Porter, W.J. / Timm, D.E. / Audia, J.E. / Barberis, M. / Beck, J.P. / Boggs, L.N. / Borders, A.R. / Boyer, R.D. ...Authors: Winneroski, L.L. / Erickson, J.A. / Green, S.J. / Lopez, J.E. / Stout, S.L. / Porter, W.J. / Timm, D.E. / Audia, J.E. / Barberis, M. / Beck, J.P. / Boggs, L.N. / Borders, A.R. / Boyer, R.D. / Brier, R.A. / Hembre, E.J. / Hendle, J. / Garcia-Losada, P. / Minguez, J.M. / Mathes, B.M. / May, P.C. / Monk, S.A. / Rankovic, Z. / Shi, Y. / Watson, B.M. / Yang, Z. / Mergott, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 352.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 283.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 581.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 586.7 KB | Display | |
Data in XML | ![]() | 2.9 KB | Display | |
Data in CIF | ![]() | 17.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uvvC ![]() 6uvyC ![]() 6uwpC ![]() 6uwvC ![]() 6bfeS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48970.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 1117 molecules ![](data/chem/img/QJJ.gif)
![](data/chem/img/QJM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/QJM.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-QJJ / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.14 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 100mM Sodium Cacodylate pH 7.4, 12% PEG 8K, 200mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→99.99 Å / Num. obs: 146798 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.56→1.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.661 / Num. unique obs: 21253 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6BFE Resolution: 1.56→30 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.711 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.064 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.44 Å2 / Biso mean: 18.445 Å2 / Biso min: 5.53 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.56→1.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|