Crystal Structure of human beta-secretase (BACE) in the presence of an inhibitor (2)

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

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This is version 1.3 of the entry. See complete history


Design of potent inhibitors of human beta-secretase. Part 2.

Freskos, J.N.Fobian, Y.M.Benson, T.E.Moon, J.B.Bienkowski, M.J.Brown, D.L.Emmons, T.L.Heintz, R.Laborde, A.McDonald, J.J.Mischke, B.V.Molyneaux, J.M.Mullins, P.B.Bryan Prince, D.Paddock, D.J.Tomasselli, A.G.Winterrowd, G.

(2007) Bioorg Med Chem Lett 17: 78-81

  • DOI: https://doi.org/10.1016/j.bmcl.2006.09.091
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We describe an optimized series of acyclic hydroxyethylamine transition state isosteres of beta-secretase that incorporates a variety of P(2) side chains that yield potent inhibitors with excellent cellular activity. A 2.2A crystal structure of compound 13 is shown.

  • Organizational Affiliation

    Pfizer Inc., 700N. Chesterfield Pkwy., St. Louis, MO 63198, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1406Homo sapiensMutation(s): 0 
Gene Names: BACE
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 LIQ

Download Ideal Coordinates CCD File 
C33 H42 F2 N4 O5 S
Binding Affinity Annotations 
IDSourceBinding Affinity
LIQ PDBBind:  2HM1 IC50: 2 (nM) from 1 assay(s)
Binding MOAD:  2HM1 IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.99α = 90
b = 104.88β = 94.99
c = 50.06γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description