2QMD

Structure of BACE Bound to SCH722924

• PDB DOI: https://doi.org/10.2210/pdb2QMD/pdb

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


• Deposited: 2007-07-16 Released: 2008-03-11 
• Deposition Author(s): Strickland, C.O., Iserloh, U.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.213 
• R-Value Work: 0.187 

Literature

Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.

Iserloh, U., Wu, Y., Cumming, J.N., Pan, J., Wang, L.Y., Stamford, A.W., Kennedy, M.E., Kuvelkar, R., Chen, X., Parker, E.M., Strickland, C., Voigt, J.

(2008) Bioorg Med Chem Lett 18: 414-417

• PubMed: 18023580 
• DOI: https://doi.org/10.1016/j.bmcl.2007.10.116
• Primary Citation of Related Structures:  
  2QK5, 2QMD, 2QMF, 2QP8


• PubMed Abstract: 
  

  Based on lead compound 1 identified from the patent literature, we developed novel patentable BACE-1 inhibitors by introducing a cyclic amine scaffold. Extensive SAR studies on both pyrrolidines and piperidines ultimately led to inhibitor 2f, one of the most potent inhibitors synthesized to date.

---

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: 89.54 kDa 
• Atom Count: 7,207 
• Modelled 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
CS7	D [auth A], F [auth B]	N'-[(1S,2R)-2-[(2R,4R)-4-(BENZYLOXY)PYRROLIDIN-2-YL]-1-(3,5-DIFLUOROBENZYL)-2-HYDROXYETHYL]-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE C35 H43 F2 N3 O4 GZHSLBYVXGDJDF-NXVJRICRSA-N
TAR	C [auth A], E [auth A], G [auth B]	D(-)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-LWMBPPNESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CS7	PDBBind:  2QMD	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.213 
• R-Value Work: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.453	α = 90
b = 89.206	β = 90
c = 131.048	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Strickland, C.O., Iserloh, U.

Revision History  

• Version 1.0: 2008-03-11
  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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary