2QMG | pdb_00002qmg

Structure of BACE Bound to SCH745966

• PDB DOI: https://doi.org/10.2210/pdb2QMG/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-07-16 Released: 2008-03-18 
• Deposition Author(s): Strickland, C.O., Iserloh, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 
  0.212 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.181 (DCC) 

Literature

Discovery of an orally efficaceous 4-phenoxypyrrolidine-based BACE-1 inhibitor.

Iserloh, U., Pan, J., Stamford, A.W., Kennedy, M.E., Zhang, Q., Zhang, L., Parker, E.M., McHugh, N.A., Favreau, L., Strickland, C., Voigt, J.

(2008) Bioorg Med Chem Lett 18: 418-422

• PubMed: 17980584 
• DOI: https://doi.org/10.1016/j.bmcl.2007.10.053
• Primary Citation Related Structures: 
  2QMG


• PubMed Abstract: 
  

  Based on a lead compound identified from the patent literature, we developed patentably novel BACE-1 inhibitors by introducing a cyclic amine scaffold as embodied by 1a and 1b. Extensive SAR studies assessed a variety of isophthalamide replacements including substituted pyrrolidinones and ultimately led to the identification of 11. Due to its favorable overall profile, 11 has been extensively profiled in various in vivo settings.

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Organizational Affiliation: 
• Department of Chemical Research, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.39 kDa 
• Atom Count: 7,141 
• Modeled Residue Count: 779 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	395	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SC6	C [auth A], E [auth B]	N-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-2-[(2R,4R)-4-PHENOXYPYRROLIDIN-2-YL]ETHYL}-3-{[(2R)-2-(METHOXYMETHYL)PYRROLIDIN-1-YL]CARBONYL}-5-METHYLBENZAMIDE C34 H39 F2 N3 O5 KYHYNSQLYDXSNK-MXWGZHRFSA-N
TAR	D [auth A], F [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free:  0.212 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.181 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.549	α = 90
b = 89.288	β = 90
c = 130.754	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Strickland, C.O., Iserloh, U.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary