Structure of BACE bound to SCH743813

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 

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Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization.

Cumming, J.Babu, S.Huang, Y.Carrol, C.Chen, X.Favreau, L.Greenlee, W.Guo, T.Kennedy, M.Kuvelkar, R.Le, T.Li, G.McHugh, N.Orth, P.Ozgur, L.Parker, E.Saionz, K.Stamford, A.Strickland, C.Tadesse, D.Voigt, J.Zhang, L.Zhang, Q.

(2010) Bioorg Med Chem Lett 20: 2837-2842

  • DOI: https://doi.org/10.1016/j.bmcl.2010.03.050
  • Primary Citation of Related Structures:  
    3LNK, 3LPI, 3LPJ, 3LPK

  • PubMed Abstract: 

    With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Abeta(40) in transgenic mice with a single subcutaneous dose.

  • Organizational Affiliation

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@merck.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
395Homo sapiensMutation(s): 0 
Gene Names: BACEBACE1KIAA1149
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 74A

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
C35 H42 F2 N4 O4
Query on TLA

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C4 H6 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
74A PDBBind:  3LNK IC50: 1150 (nM) from 1 assay(s)
BindingDB:  3LNK IC50: 1150 (nM) from 1 assay(s)
Binding MOAD:  3LNK IC50: 1150 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.364α = 90
b = 89.37β = 90
c = 131.511γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data 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: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description