Crystal Structure of Human BACE-1 in Complex with CNP520

Experimental Data Snapshot

  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.15252/emmm.201809316
  • Primary Citation of Related Structures:  

  • 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

    Musculoskeletal Diseases, Novartis Institute for BioMedical Research, Basel, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1402Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BUH (Subject of Investigation/LOI)
Query on BUH

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
BUH BindingDB:  6EQM IC50: min: 3, max: 11 (nM) from 3 assay(s)
Binding MOAD:  6EQM IC50: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.35 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.66α = 90
b = 76.65β = 90
c = 104.54γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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