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- PDB-5ezz: CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH (4S)-4-[3-(5-chloro-3... -

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Basic information

Entry
Database: PDB / ID: 5ezz
TitleCRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH (4S)-4-[3-(5-chloro-3-pyridyl)phenyl]-4-[4-(difluoromethoxy)-3-methyl-phenyl]-5H-oxazol-2-amine
ComponentsBeta-secretase 1
KeywordsHydrolase/Inhibitor / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / Hydrolase-Inhibitor complex
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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion ...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 / detection of mechanical stimulus involved in sensory perception of pain / amyloid-beta metabolic process / cellular response to manganese ion / prepulse inhibition / 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 / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / late endosome / synaptic vesicle / 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
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5T6 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsBanner, D. / Benz, J. / Stihle, M. / Kuglstatter, A.
CitationJournal: J.Med.Chem. / Year: 2016
Title: A Real-World Perspective on Molecular Design.
Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / ...Authors: Kuhn, B. / Guba, W. / Hert, J. / Banner, D. / Bissantz, C. / Ceccarelli, S. / Haap, W. / Korner, M. / Kuglstatter, A. / Lerner, C. / Mattei, P. / Neidhart, W. / Pinard, E. / Rudolph, M.G. / Schulz-Gasch, T. / Woltering, T. / Stahl, M.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9665
Polymers43,4121
Non-polymers5544
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-16 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.670, 102.670, 170.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Beta-secretase 1 / Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP ...Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Memapsin-2 / Membrane-associated aspartic protease 2


Mass: 43411.895 Da / Num. of mol.: 1 / Mutation: K307A
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
#2: Chemical ChemComp-5T6 / (4~{S})-4-[4-[bis(fluoranyl)methoxy]-3-methyl-phenyl]-4-[3-(5-chloranylpyridin-3-yl)phenyl]-5~{H}-1,3-oxazol-2-amine


Mass: 429.847 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18ClF2N3O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5M SODIUM FORMATE, 100MM HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.84 Å / Num. obs: 29742 / % possible obs: 99.6 % / Redundancy: 10.57 % / Rsym value: 0.0529 / Net I/σ(I): 13.16
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 10.11 % / Rmerge(I) obs: 0.5011 / Mean I/σ(I) obs: 2.07 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→47.84 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.447 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23957 1608 5.1 %RANDOM
Rwork0.20467 ---
obs0.2065 29742 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.454 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0.24 Å20 Å2
2---0.48 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 36 262 3277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9574205
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4675377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38423.759141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9141518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212380
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7681.51885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40723040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63131211
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7444.51165
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 124 -
Rwork0.314 1996 -
obs--93.02 %

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