6EQM | pdb_00006eqm

Crystal Structure of Human BACE-1 in Complex with CNP520

• PDB DOI: https://doi.org/10.2210/pdb6EQM/pdb

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


• Deposited: 2017-10-13 Released: 2018-09-19 
• Deposition Author(s): Rondeau, J.-M., Wirth, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: other

Literature

The BACE-1 inhibitor CNP520 for prevention trials in Alzheimer's disease.

Neumann, U., Ufer, M., Jacobson, L.H., Rouzade-Dominguez, M.L., Huledal, G., Kolly, C., Luond, R.M., Machauer, R., Veenstra, S.J., Hurth, K., Rueeger, H., Tintelnot-Blomley, M., Staufenbiel, M., Shimshek, D.R., Perrot, L., Frieauff, W., Dubost, V., Schiller, H., Vogg, B., Beltz, K., Avrameas, A., Kretz, S., Pezous, N., Rondeau, J.M., Beckmann, N., Hartmann, A., Vormfelde, S., David, O.J., Galli, B., Ramos, R., Graf, A., Lopez Lopez, C.

(2018) EMBO Mol Med 10

• PubMed: 30224383 
• DOI: https://doi.org/10.15252/emmm.201809316
• Primary Citation Related Structures: 
  6EQM


• PubMed Abstract: 
  

  The beta-site amyloid precursor protein cleaving enzyme-1 (BACE-1) initiates the generation of amyloid-β (Aβ), and the amyloid cascade leading to amyloid plaque deposition, neurodegeneration, and dementia in Alzheimer's disease (AD). Clinical failures of anti-Aβ therapies in dementia stages suggest that treatment has to start in the early, asymptomatic disease states. The BACE-1 inhibitor CNP520 has a selectivity, pharmacodynamics, and distribution profile suitable for AD prevention studies. CNP520 reduced brain and cerebrospinal fluid (CSF) Aβ in rats and dogs, and Aβ plaque deposition in APP-transgenic mice. Animal toxicology studies of CNP520 demonstrated sufficient safety margins, with no signs of hair depigmentation, retina degeneration, liver toxicity, or cardiovascular effects. In healthy adults ≥ 60 years old, treatment with CNP520 was safe and well tolerated and resulted in robust and dose-dependent Aβ reduction in the cerebrospinal fluid. Thus, long-term, pivotal studies with CNP520 have been initiated in the Generation Program.

---

Organizational Affiliation: 
• Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland [e-mail] [e-mail].
Translational Medicine, Novartis Institute for BioMedical Research, Basel, Switzerland.
Neuroscience, Novartis Institute for BioMedical Research, Basel, Switzerland.
PK Sciences, Novartis Institute for BioMedical Research, Basel, Switzerland.
Preclinical Safety, Novartis Institute for BioMedical Research, Basel, Switzerland.
Global Discovery Chemistry, Novartis Institute for BioMedical Research, Basel, Switzerland.
Biomarker Discovery, Novartis Institute for BioMedical Research, Basel, Switzerland.
Chemical Biology and Therapeutics, Novartis Institute for BioMedical Research, Basel, Switzerland.
Musculoskeletal Diseases, Novartis Institute for BioMedical Research, Basel, Switzerland.
Global Drug Development, Novartis, Basel, Switzerland.
Global Drug Development, Novartis, Basel, Switzerland [e-mail] [e-mail].

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: 45.29 kDa 
• Atom Count: 3,382 
• Modeled Residue Count: 378 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	402	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BUH (Subject of Investigation/LOI)	B [auth A]	~{N}-[6-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]-5-fluoranyl-pyridin-2-yl]-3-chloranyl-5-(trifluoromethyl)pyridine-2-carboxamide C19 H15 Cl F7 N5 O2 PSBBWFNMHDUTRH-DLBZAZTESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BUH	BindingDB:  6EQM	IC50: min: 3, max: 11 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.66	α = 90
b = 76.65	β = 90
c = 104.54	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Rondeau, J.-M., Wirth, E.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2018-09-26
  Changes: Data collection, Database references
• Version 1.2: 2018-11-21
  Changes: Data collection, Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary