Structure of beta-secretase complexed with inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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Structure-based design of highly selective beta-secretase inhibitors: synthesis, biological evaluation, and protein-ligand X-ray crystal structure.

Ghosh, A.K.Venkateswara Rao, K.Yadav, N.D.Anderson, D.D.Gavande, N.Huang, X.Terzyan, S.Tang, J.

(2012) J Med Chem 55: 9195-9207

  • DOI: https://doi.org/10.1021/jm3008823
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure-based design, synthesis, and X-ray structure of protein-ligand complexes of exceptionally potent and selective β-secretase inhibitors are described. The inhibitors are designed specifically to interact with S(1)' active site residues to provide selectivity over memapsin 1 and cathepsin D. Inhibitor 5 has exhibited exceedingly potent inhibitory activity (K(i) = 17 pM) and high selectivity over BACE 2 (>7000-fold) and cathepsin D (>250000-fold). A protein-ligand crystal structure revealed important molecular insight into these selectivities. These interactions may serve as an important guide to design selectivity over the physiologically important aspartic acid proteases.

  • Organizational Affiliation

    Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States. akghosh@purdue.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C, D
388Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
0GH PDBBind:  4GID Ki: 0.02 (nM) from 1 assay(s)
BindingDB:  4GID Ki: 99 (nM) from 1 assay(s)
IC50: 1000 (nM) from 1 assay(s)
Binding MOAD:  4GID Ki: 0.02 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.427α = 90
b = 130.353β = 97.5
c = 88.401γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description