+Open data
-Basic information
Entry | Database: PDB / ID: 3l38 | ||||||
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Title | Bace1 in complex with the aminopyridine Compound 44 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / beta-secretase / bace-1 / aminopyridine / inhibitor / Aspartyl protease / Disulfide bond / Protease / Transmembrane / Zymogen | ||||||
Function / homology | Function and homology information 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 / prepulse inhibition / amyloid-beta metabolic process ...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 / prepulse inhibition / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / 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 / amyloid-beta binding / peptidase activity / endopeptidase activity / amyloid fibril formation / lysosome / aspartic-type endopeptidase activity / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / axon / endoplasmic reticulum lumen / dendrite / neuronal cell body / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Olland, A.M. / Chopra, R. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Novel pyrrolyl 2-aminopyridines as potent and selective human beta-secretase (BACE1) inhibitors. Authors: Malamas, M.S. / Barnes, K. / Hui, Y. / Johnson, M. / Lovering, F. / Condon, J. / Fobare, W. / Solvibile, W. / Turner, J. / Hu, Y. / Manas, E.S. / Fan, K. / Olland, A. / Chopra, R. / Bard, J. ...Authors: Malamas, M.S. / Barnes, K. / Hui, Y. / Johnson, M. / Lovering, F. / Condon, J. / Fobare, W. / Solvibile, W. / Turner, J. / Hu, Y. / Manas, E.S. / Fan, K. / Olland, A. / Chopra, R. / Bard, J. / Pangalos, M.N. / Reinhart, P. / Robichaud, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l38.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l38.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 3l38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l38 ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l38 | HTTPS FTP |
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-Related structure data
Related structure data | 3l3aC 1w50S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 46440.980 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 46-454) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2 |
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#2: Chemical | ChemComp-879 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: Oct 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 19839 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1W50.pdb Resolution: 2.1→19.927 Å / SU ML: 0.29 / σ(F): 1.34 / 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: 24.315 Å2 / ksol: 0.389 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.927 Å
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Refine LS restraints |
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LS refinement shell |
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