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- PDB-2q11: Structure of BACE complexed to compound 1 -

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Basic information

Entry
Database: PDB / ID: 2q11
TitleStructure of BACE complexed to compound 1
ComponentsBeta-secretase 1
KeywordsHYDROLASE / BACE 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 / 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
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-XX4 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSharff, A.J.
CitationJournal: J.Med.Chem. / Year: 2007
Title: 2-Amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (beta-Site APP cleaving enzyme): Use of structure based design to convert a micromolar hit into a nanomolar lead.
Authors: Baxter, E.W. / Conway, K.A. / Kennis, L. / Bischoff, F. / Mercken, M.H. / Winter, H.L. / Reynolds, C.H. / Tounge, B.A. / Luo, C. / Scott, M.K. / Huang, Y. / Braeken, M. / Pieters, S.M. / ...Authors: Baxter, E.W. / Conway, K.A. / Kennis, L. / Bischoff, F. / Mercken, M.H. / Winter, H.L. / Reynolds, C.H. / Tounge, B.A. / Luo, C. / Scott, M.K. / Huang, Y. / Braeken, M. / Pieters, S.M. / Berthelot, D.J. / Masure, S. / Bruinzeel, W.D. / Jordan, A.D. / Parker, M.H. / Boyd, R.E. / Qu, J. / Alexander, R.S. / Brenneman, D.E. / Reitz, A.B.
History
DepositionMay 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1916
Polymers129,9363
Non-polymers1,2563
Water7,332407
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7302
Polymers43,3121
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7302
Polymers43,3121
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7302
Polymers43,3121
Non-polymers4191
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.9, 108.5, 63.1
Angle α, β, γ (deg.)90.0, 102.94, 90.0
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a monomer. There are three monomers in the asymmetric unit

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Components

#1: Protein Beta-secretase 1 / Beta-site APP cleaving enzyme 1


Mass: 43311.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE / Production host: unidentified baculovirus / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-XX4 / 3-(2-AMINO-6-BENZOYLQUINAZOLIN-3(4H)-YL)-N-CYCLOHEXYL-N-METHYLPROPANAMIDE


Mass: 418.531 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H30N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEGMME5K 0.2 M Ammonium Iodide, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
DetectorDate: Sep 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→500 Å / Num. all: 60608 / Num. obs: 59364 / Rsym value: 0.071
Reflection shellHighest resolution: 2.4 Å / Rsym value: 0.38

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→500 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.337 2996 -RANDOM
Rwork0.278 ---
all-60608 --
obs-59364 97.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9147 0 93 407 9647

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