Crystal structure of human Beta Secretase complexed with I21

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Strategies toward improving the brain penetration of macrocyclic tertiary carbinamine BACE-1 inhibitors.

Moore, K.P.Zhu, H.Rajapakse, H.A.McGaughey, G.B.Colussi, D.Price, E.A.Sankaranarayanan, S.Simon, A.J.Pudvah, N.T.Hochman, J.H.Allison, T.Munshi, S.K.Graham, S.L.Vacca, J.P.Nantermet, P.G.

(2007) Bioorg Med Chem Lett 17: 5831-5835

  • DOI: https://doi.org/10.1016/j.bmcl.2007.08.040
  • Primary Citation of Related Structures:  
    2PH8, 2QZK

  • PubMed Abstract: 

    This letter describes replacements for the P3 amide moiety present in previously reported tertiary carbinamine macrolactones. Although P-gp efflux issues associated with these amide-macrolactones were solved and full brain penetration was measured in one case, potency was compromised in the process.

  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. keith_moore2@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1405Homo sapiensMutation(s): 2 
Gene Names: BACE1BACE
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on I21

Download Ideal Coordinates CCD File 
B [auth A]2-[(5R)-5-amino-5-methyl-4,16-dioxo-14-phenyl-3-oxa-15-azatricyclo[,11~]docosa-1(21),7(22),8,10,12,14,17,19-octaen-19-yl]benzonitrile
C34 H27 N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
I21 PDBBind:  2QZK IC50: 27 (nM) from 1 assay(s)
Binding MOAD:  2QZK IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.685α = 90
b = 127.495β = 90
c = 76.41γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2008-04-29 
  • Deposition Author(s): Munshi, S.

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description