4DJX

Structure of BACE Bound to 5-(3-(5-chloropyridin-3-yl)phenyl)-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one

• PDB DOI: https://doi.org/10.2210/pdb4DJX/pdb

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


• Deposited: 2012-02-02 Released: 2012-03-21 
• Deposition Author(s): Strickland, C., Cumming, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor.

Cumming, J.N., Smith, E.M., Wang, L., Misiaszek, J., Durkin, J., Pan, J., Iserloh, U., Wu, Y., Zhu, Z., Strickland, C., Voigt, J., Chen, X., Kennedy, M.E., Kuvelkar, R., Hyde, L.A., Cox, K., Favreau, L., Czarniecki, M.F., Greenlee, W.J., McKittrick, B.A., Parker, E.M., Stamford, A.W.

(2012) Bioorg Med Chem Lett 22: 2444-2449

• PubMed: 22390835 
• DOI: https://doi.org/10.1016/j.bmcl.2012.02.013
• Primary Citation of Related Structures:  
  4DJU, 4DJV, 4DJW, 4DJX, 4DJY


• PubMed Abstract: 
  

  From an initial lead 1, a structure-based design approach led to identification of a novel, high-affinity iminohydantoin BACE1 inhibitor that lowers CNS-derived Aβ following oral administration to rats. Herein we report SAR development in the S3 and F' subsites of BACE1 for this series, the synthetic approaches employed in this effort, and in vivo data for the optimized compound.

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Organizational Affiliation: 

Merck Research Laboratories, 2000 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: 93.48 kDa 
• Atom Count: 7,115 
• Modelled Residue Count: 779 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	414	Homo sapiens	Mutation(s): 0  Gene Names: BACE, BACE1, KIAA1149 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
0KQ	C [auth A], E [auth B]	(2E,5R)-5-[3-(5-chloropyridin-3-yl)phenyl]-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one C18 H17 Cl N4 O SZDQNTKTWBPIBH-GOSISDBHSA-N
TLA	D [auth A], F [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0KQ	PDBBind:  4DJX	Ki: 59 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.471	α = 90
b = 89.462	β = 90
c = 131.225	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
CNS	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Strickland, C., Cumming, J.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary