6WNY | pdb_00006wny

Crystal structure of BACE1 in complex with (Z)-fluoro-olefin containing compound 15

• PDB DOI: https://doi.org/10.2210/pdb6WNY/pdb

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


• Deposited: 2020-04-23 Released: 2020-06-03 
• Deposition Author(s): Whittington, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The development of a structurally distinct series of BACE1 inhibitors via the (Z)-fluoro-olefin amide bioisosteric replacement.

Frohn, M., Liu, L., Siegmund, A.C., Qian, W., Amegadzie, A., Chen, N., Tan, H., Hickman, D., Wood, S., Wen, P.H., Bartberger, M.D., Whittington, D.A., Allen, J.R., Bourbeau, M.P.

(2020) Bioorg Med Chem Lett 30: 127240-127240

• PubMed: 32527542 
• DOI: https://doi.org/10.1016/j.bmcl.2020.127240
• Primary Citation Related Structures: 
  6WNY


• PubMed Abstract: 
  

  The (Z)-fluoro-olefin amide bioisosteric replacement is an effective tool for addressing various shortcomings of the parent amide. In an effort to fine tune ADME properties of BACE1 preclinical candidate AM-6494, a series of structurally distinct (Z)-fluoro-olefin containing analogs was developed that culminated in compound 15. Herein, we detail design considerations, synthetic challenges, structure activity relationship (SAR) studies, and in vivo properties of an advanced compound in this novel series of BACE1 inhibitors.

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Organizational Affiliation: 
• Medicinal Chemistry, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States. Electronic address: [e-mail].
Medicinal Chemistry, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States.
Pre-Pivotal Drug Product, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States.
Pharmicokinetics and Drug Metabolism, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States.
Neuroscience Research, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States.
Molecular Engineering, Amgen Discovery Research, Amgen Inc., Thousand Oaks, CA 91320, United States.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.7 kDa 
• Atom Count: 3,429 
• Modeled Residue Count: 380 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	411	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
U64 (Subject of Investigation/LOI)	B [auth A]	6-[(Z)-2-{3-[(1S,5S,6S)-3-amino-5-methyl-1-(morpholine-4-carbonyl)-2-thia-4-azabicyclo[4.1.0]hept-3-en-5-yl]-4-fluorophenyl}-1-fluoroethenyl]pyridine-3-carbonitrile C25 H23 F2 N5 O2 S VZHFJCNPAIRJSA-MYMUPAQMSA-N
IOD	C [auth A], D [auth A], E [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
U64	BindingDB:  6WNY	IC50: min: 1.5, max: 2 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.783	α = 90
b = 101.783	β = 90
c = 171.141	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Whittington, D.A.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-06-24
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary