+Open data
-Basic information
Entry | Database: PDB / ID: 3cic | ||||||
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Title | Structure of BACE Bound to SCH709583 | ||||||
Components | Beta-secretase 1 | ||||||
Keywords | HYDROLASE / BACE1 / Aspartyl protease | ||||||
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 / 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 / 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 / lysosome / aspartic-type endopeptidase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.75 Å | ||||||
Authors | Strickland, C. / Cumming, J. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2008 Title: Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors Authors: Cumming, J.N. / Le, T.X. / Babu, S. / Carroll, C. / Chen, X. / Favreau, L. / Gaspari, P. / Guo, T. / Hobbs, D.W. / Huang, Y. / Iserloh, U. / Kennedy, M.E. / Kuvelkar, R. / Li, G. / Lowrie, J. ...Authors: Cumming, J.N. / Le, T.X. / Babu, S. / Carroll, C. / Chen, X. / Favreau, L. / Gaspari, P. / Guo, T. / Hobbs, D.W. / Huang, Y. / Iserloh, U. / Kennedy, M.E. / Kuvelkar, R. / Li, G. / Lowrie, J. / McHugh, N.A. / Ozgur, L. / Pan, J. / Parker, E.M. / Saionz, K. / Stamford, A.W. / Strickland, C. / Tadesse, D. / Voigt, J. / Wang, L. / Wu, Y. / Zhang, L. / Zhang, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cic.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cic.ent.gz | 150.4 KB | Display | PDB format |
PDBx/mmJSON format | 3cic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3cic ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3cic | HTTPS FTP |
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-Related structure data
Related structure data | 3cibC 3cidC 2qkj C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43425.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 102118 / Num. obs: 101817 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Χ2: 1.446 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.6 / Num. unique all: 10071 / Rsym value: 0.391 / Χ2: 1.265 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.75→50 Å / FOM work R set: 0.835 / σ(F): 0 / σ(I): 0
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Displacement parameters | Biso mean: 22.133 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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Xplor file |
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