Crystal Structure of BACE with Compound 12a

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Spirocyclic sulfamides as beta-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer's disease: utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors.

Brodney, M.A.Barreiro, G.Ogilvie, K.Hajos-Korcsok, E.Murray, J.Vajdos, F.Ambroise, C.Christoffersen, C.Fisher, K.Lanyon, L.Liu, J.Nolan, C.E.Withka, J.M.Borzilleri, K.A.Efremov, I.Oborski, C.E.Varghese, A.O'Neill, B.T.

(2012) J Med Chem 55: 9224-9239

  • DOI: https://doi.org/10.1021/jm3009426
  • Primary Citation of Related Structures:  
    4FM7, 4FM8

  • PubMed Abstract: 

    β-Secretase 1 (BACE-1) is an attractive therapeutic target for the treatment and prevention of Alzheimer's disease (AD). Herein, we describe the discovery of a novel class of BACE-1 inhibitors represented by sulfamide 14g, using a medicinal chemistry strategy to optimize central nervous system (CNS) penetration by minimizing hydrogen bond donors (HBDs) and reducing P-glycoprotein (P-gp) mediated efflux. We have also taken advantage of the combination of structure based drug design (SBDD) to guide the optimization of the sulfamide analogues and the in silico tool WaterMap to explain the observed SAR. Compound 14g is a potent inhibitor of BACE-1 with excellent permeability and a moderate P-gp liability. Administration of 14g to mice produced a significant, dose-dependent reduction in central Aβ(X-40) levels at a free drug exposure equivalent to the whole cell IC(50) (100 nM). Furthermore, studies of the P-gp knockout mouse provided evidence that efflux transporters affected the amount of Aβ lowering versus that observed in wild-type (WT) mouse at an equivalent dose.

  • Organizational Affiliation

    Department of Neuroscience, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. michael.a.brodney@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1404Homo 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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 0UQ

Download Ideal Coordinates CCD File 
B [auth A](5R,7S)-1-(3-fluorophenyl)-3,7-dimethyl-8-[3-(propan-2-yloxy)benzyl]-2-thia-1,3,8-triazaspiro[4.5]decane 2,2-dioxide
C24 H32 F N3 O3 S
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
0UQ BindingDB:  4FM8 IC50: min: 1800, max: 2400 (nM) from 2 assay(s)
Binding MOAD:  4FM8 IC50: 2400 (nM) from 1 assay(s)
PDBBind:  4FM8 IC50: 2400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.719α = 90
b = 103.262β = 90
c = 98.619γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references