4R91

BACE-1 in complex with (R)-4-(2-cyclohexylethyl)-4-(((1S,3R)-3-(cyclopentylamino)cyclohexyl)methyl)-1-methyl-5-oxoimidazolidin-2-iminium

• PDB DOI: https://doi.org/10.2210/pdb4R91/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-03 Released: 2014-11-05 
• Deposition Author(s): Orth, P., Caldwell, J.P., Strickland, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.213 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Discovery of potent iminoheterocycle BACE1 inhibitors.

Caldwell, J.P., Mazzola, R.D., Durkin, J., Chen, J., Chen, X., Favreau, L., Kennedy, M., Kuvelkar, R., Lee, J., McHugh, N., McKittrick, B., Orth, P., Stamford, A., Strickland, C., Voigt, J., Wang, L., Zhang, L., Zhang, Q., Zhu, Z.

(2014) Bioorg Med Chem Lett 24: 5455-5459

• PubMed: 25455483 
• DOI: https://doi.org/10.1016/j.bmcl.2014.10.006
• Primary Citation of Related Structures:  
  4R8Y, 4R91, 4R92, 4R93, 4R95


• PubMed Abstract: 
  

  The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select compounds from this subset acutely lowered Aβ40 levels upon subcutaneous and oral administration to rats.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. Electronic address: [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: 93.61 kDa 
• Atom Count: 7,001 
• Modelled Residue Count: 773 
• 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: BACE1, BACE, 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
3KT	D [auth A], F [auth B]	(2E,5R)-5-(2-cyclohexylethyl)-5-{[(1S,3R)-3-(cyclopentylamino)cyclohexyl]methyl}-2-imino-3-methylimidazolidin-4-one C24 H42 N4 O NOZCXTAZEGFFAQ-XZDHIHRUSA-N
TLA	C [auth A], E [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3KT	BindingDB:  4R91	Ki: 430 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.213 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.41	α = 90
b = 89.55	β = 90
c = 131.07	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Orth, P., Caldwell, J.P., Strickland, C.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary