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- PDB-6ej3: BACE1 compound 23 -

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Basic information

Entry
Database: PDB / ID: 6ej3
TitleBACE1 compound 23
ComponentsBeta-secretase 1
KeywordsPEPTIDE BINDING PROTEIN / BACE1 / protease / Alzheimer
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 / 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 / late endosome / synaptic vesicle / 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
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-B7T / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsJohansson, P.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Toward beta-Secretase-1 Inhibitors with Improved Isoform Selectivity.
Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / ...Authors: Johansson, P. / Kaspersson, K. / Gurrell, I.K. / Back, E. / Eketjall, S. / Scott, C.W. / Cebers, G. / Thorne, P. / McKenzie, M.J. / Beaton, H. / Davey, P. / Kolmodin, K. / Holenz, J. / Duggan, M.E. / Budd Haeberlein, S. / Burli, R.W.
History
DepositionSep 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,1932
Polymers55,8151
Non-polymers3771
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.889, 102.889, 170.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-783-

HOH

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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: 55815.492 Da / Num. of mol.: 1
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-B7T / (1r,4r)-4-methoxy-6'-(5-methyl-3-pyridinyl)-3'H-dispiro[cyclohexane-1,2'-indene-1',4''-[1,3]oxazol]-2''-amine


Mass: 377.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C23H27N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 11% PEG 6k, 100mM NaOAc pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.94→47.84 Å / Num. obs: 40169 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 44.99 Å2 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.05 / Net I/σ(I): 10.1
Reflection shellResolution: 1.94→2.01 Å / Rmerge(I) obs: 4.35 / Rpim(I) all: 1

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
MOSFLMdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house structure

Resolution: 1.94→47.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.12 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2004 5.02 %RANDOM
Rwork0.194 ---
obs0.195 39951 99.7 %-
Displacement parametersBiso mean: 54.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.88 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.94→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 28 185 3114
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0123014HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.194104HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d999SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes444HARMONIC5
X-RAY DIFFRACTIONt_it3014HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3409SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2311 127 4.57 %
Rwork0.2284 2654 -
all0.2285 2781 -
obs--96.12 %
Refinement TLS params.Method: refined / Origin x: -14.4979 Å / Origin y: -42.0101 Å / Origin z: 0.5109 Å
111213212223313233
T-0.2597 Å2-0.0084 Å2-0.0331 Å2--0.2491 Å2-0.018 Å2---0.2425 Å2
L2.5247 °2-1.3631 °21.1183 °2-0.8844 °2-0.5748 °2--1.218 °2
S-0.0114 Å °0.048 Å °-0.278 Å °-0.001 Å °0.0429 Å °0.1655 Å °-0.0609 Å °0.0629 Å °-0.0315 Å °
Refinement TLS groupSelection details: { A|* }

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