4RRN

8-Tetrahydropyran-2-yl chromans: highly selective beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb4RRN/pdb

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


• Deposited: 2014-11-06 Released: 2014-12-03 
• Deposition Author(s): Thomas, A.A., Hunt, K.W., Newhouse, B., Watts, R.J., Liu, X., Vigers, G.P.A., Smith, D., Rhodes, S.P., Brown, K.D., Otten, J.N., Burkard, M., Cox, A.A., Geck Do, M.K., Dutcher, D., Rana, S., DeLisle, R.K., Regal, K., Wright, A.D., Groneberg, R., Liao, J., Scearce-Levie, K., Siu, M., Purkey, H.E., Lyssikatos, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

8-Tetrahydropyran-2-yl Chromans: Highly Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors.

Thomas, A.A., Hunt, K.W., Newhouse, B., Watts, R.J., Liu, X., Vigers, G., Smith, D., Rhodes, S.P., Brown, K.D., Otten, J.N., Burkard, M., Cox, A.A., Geck Do, M.K., Dutcher, D., Rana, S., DeLisle, R.K., Regal, K., Wright, A.D., Groneberg, R., Liao, J., Scearce-Levie, K., Siu, M., Purkey, H.E., Lyssikatos, J.P.

(2014) J Med Chem 57: 10112-10129

• PubMed: 25411915 
• DOI: https://doi.org/10.1021/jm5015132
• Primary Citation of Related Structures:  
  4R5N, 4RRN, 4RRO, 4RRS


• PubMed Abstract: 
  

A series of 2,3,4,4a,10,10a-hexahydropyrano[3,2-b]chromene analogs was developed that demonstrated high selectivity (>2000-fold) for BACE1 vs Cathepsin D (CatD). Three different Asp-binding moieties were examined: spirocyclic acyl guanidines, aminooxazolines, and aminothiazolines in order to modulate potency, selectivity, efflux, and permeability. Guided by structure based design, changes to P2' and P3 moieties were explored. A conformationally restricted P2' methyl group provided inhibitors with excellent cell potency (37-137 nM) and selectivity (435 to >2000-fold) for BACE1 vs CatD. These efforts lead to compound 59, which demonstrated a 69% reduction in rat CSF Aβ1-40 at 60 mg/kg (PO).

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Organizational Affiliation: 

Array BioPharma, 3200 Walnut Street, Boulder, Colorado 80301, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 45.89 kDa 
• Atom Count: 3,438 
• Modelled Residue Count: 393 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	406	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UW	C [auth A]	(4S,4a'S,10a'R)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-2'H-spiro[imidazole-4,10'-pyrano[3,2-b]chromen]-5(1H)-one C20 H19 F N4 O3 GZRDWAATBYKNGI-FTRWYGJKSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3UW	BindingDB:  4RRN	IC50: min: 12, max: 48 (nM) from 2 assay(s)
	Binding MOAD:  4RRN	IC50: 48 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.47	α = 90
b = 103.84	β = 90
c = 100.3	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): Thomas, A.A., Hunt, K.W., Newhouse, B., Watts, R.J., Liu, X., Vigers, G.P.A., Smith, D., Rhodes, S.P., Brown, K.D., Otten, J.N., Burkard, M., Cox, A.A., Geck Do, M.K., Dutcher, D., Rana, S., DeLisle, R.K., Regal, K., Wright, A.D., Groneberg, R., Liao, J., Scearce-Levie, K., Siu, M., Purkey, H.E., Lyssikatos, J.P.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references