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- PDB-4b00: Design and Synthesis of BACE1 Inhibitors with In Vivo Brain Reduc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b00 | ||||||
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Title | Design and Synthesis of BACE1 Inhibitors with In Vivo Brain Reduction of beta-Amyloid Peptides (COMPOUND (R)-41) | ||||||
![]() | BETA-SECRETASE 1 | ||||||
![]() | HYDROLASE / AMINOISOINDOLE / ALZHEIMER'S DISEASE | ||||||
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 / protein processing / recycling endosome / 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 | ![]() ![]() | ||||||
![]() | Swahn, B.M. / Kolmodin, K. / Karlstrom, S. / von Berg, S. / Soderman, P. / Holenz, J. / Berg, S. / Lindstrom, J. / Sundstrom, M. / Turek, D. ...Swahn, B.M. / Kolmodin, K. / Karlstrom, S. / von Berg, S. / Soderman, P. / Holenz, J. / Berg, S. / Lindstrom, J. / Sundstrom, M. / Turek, D. / Kihlstrom, J. / Slivo, C. / Andersson, L. / Pyring, D. / Ohberg, L. / Kers, A. / Bogar, K. / Bergh, M. / Olsson, L.L. / Janson, J. / Eketjall, S. / Georgievska, B. / Jeppsson, F. / Falting, J. | ||||||
![]() | ![]() Title: Design and synthesis of beta-site amyloid precursor protein cleaving enzyme (BACE1) inhibitors with in vivo brain reduction of beta-amyloid peptides. Authors: Swahn, B.M. / Kolmodin, K. / Karlstrom, S. / von Berg, S. / Soderman, P. / Holenz, J. / Berg, S. / Lindstrom, J. / Sundstrom, M. / Turek, D. / Kihlstrom, J. / Slivo, C. / Andersson, L. / ...Authors: Swahn, B.M. / Kolmodin, K. / Karlstrom, S. / von Berg, S. / Soderman, P. / Holenz, J. / Berg, S. / Lindstrom, J. / Sundstrom, M. / Turek, D. / Kihlstrom, J. / Slivo, C. / Andersson, L. / Pyring, D. / Rotticci, D. / Ohberg, L. / Kers, A. / Bogar, K. / von Kieseritzky, F. / Bergh, M. / Olsson, L.L. / Janson, J. / Eketjall, S. / Georgievska, B. / Jeppsson, F. / Falting, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.9 KB | Display | ![]() |
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PDB format | ![]() | 75 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 742.3 KB | Display | ![]() |
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Full document | ![]() | 743.5 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 29.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4azyC ![]() 1fknS S: Starting model for refinement C: citing same article ( |
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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: 45822.445 Da / Num. of mol.: 1 / Fragment: RESIDUES 43-453 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-I6X / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | PROPEPTIDE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40 % Description: RIGID BODY REFINEMENT USING REFMAC5 AND A PREVIOUSLY DETERMINED BACE1 STRUCTURE BASED ON THE PUBLISHED 1FKN STRUCTURE |
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Crystal grow | pH: 5 Details: 11% PEG6K, 90 MM NAAC PH 5.0, 18 MM TRIS PH 8.5, 135 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→43.08 Å / Num. obs: 34330 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.05 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.83→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PREVIOUSLY DETERMINED BACE1 STRUCTURE BASED ON PDB ENTRY 1FKN Resolution: 1.83→43.08 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.9086 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.139 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.13 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 26.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.188 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→43.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.89 Å / Total num. of bins used: 17
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