X-ray structure of Bace-1 in complex with compound 3.b.10

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Acylguanidine inhibitors of beta-secretase: optimization of the pyrrole ring substituents extending into the S1 and S3 substrate binding pockets.

Cole, D.C.Stock, J.R.Chopra, R.Cowling, R.Ellingboe, J.W.Fan, K.Y.Harrison, B.L.Hu, Y.Jacobsen, S.Jennings, L.D.Jin, G.Lohse, P.A.Malamas, M.S.Manas, E.S.Moore, W.J.O'Donnell, M.M.Olland, A.M.Robichaud, A.J.Svenson, K.Wu, J.Wagner, E.Bard, J.

(2008) Bioorg Med Chem Lett 18: 1063-1066

  • DOI: https://doi.org/10.1016/j.bmcl.2007.12.010
  • Primary Citation of Related Structures:  
    2ZDZ, 2ZE1

  • PubMed Abstract: 

    Proteolytic cleavage of amyloid precursor protein by beta-secretase (BACE-1) and gamma-secretase leads to formation of beta-amyloid (A beta) a key component of amyloid plaques, which are considered the hallmark of Alzheimer's disease. Small molecule inhibitors of BACE-1 may reduce levels of A beta and thus have therapeutic potential for treating Alzheimer's disease. We recently reported the identification of a novel small molecule BACE-1 inhibitor N-[2-(2,5-diphenyl-pyrrol-1-yl)-acetyl]guanidine (3.a.1). We report here the initial hit-to-lead optimization of this hit and the SAR around the aryl groups occupying the S(1) and S(2') pockets leading to submicromolar BACE-1 inhibitors.

  • Organizational Affiliation

    Chemical & Screening Sciences, Wyeth Research, 401 N. Middletown Road, Pearl River, NY 10965, USA. coledc@wyeth.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1415Homo 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
Query on 310

Download Ideal Coordinates CCD File 
B [auth A]N-carbamimidoyl-2-[2-(2-chlorophenyl)-5-[4-(4-ethanoylphenoxy)phenyl]pyrrol-1-yl]ethanamide
C27 H23 Cl N4 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
310 BindingDB:  2ZDZ IC50: min: 160, max: 3800 (nM) from 3 assay(s)
Binding MOAD:  2ZDZ IC50: 700 (nM) from 1 assay(s)
PDBBind:  2ZDZ IC50: 700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.308α = 90
b = 105.213β = 94.98
c = 50.999γ = 90
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance