Structure of BACE Bound to SCH709583

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 

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This is version 1.2 of the entry. See complete history


Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors

Cumming, J.N.Le, T.X.Babu, S.Carroll, C.Chen, X.Favreau, L.Gaspari, P.Guo, T.Hobbs, D.W.Huang, Y.Iserloh, U.Kennedy, M.E.Kuvelkar, R.Li, G.Lowrie, J.McHugh, N.A.Ozgur, L.Pan, J.Parker, E.M.Saionz, K.Stamford, A.W.Strickland, C.Tadesse, D.Voigt, J.Wang, L.Wu, Y.Zhang, L.Zhang, Q.

(2008) Bioorg Med Chem Lett 18: 3236-3241

  • DOI: https://doi.org/10.1016/j.bmcl.2008.04.050
  • Primary Citation of Related Structures:  
    3CIB, 3CIC, 3CID

  • PubMed Abstract: 

    Guided by structure-based design, we synthesized two novel series of potent inhibitors of BACE1 and generated extensive SAR around both the prime and non-prime side binding pockets. The key feature of both series is a cyclic amine motif specifically crafted to achieve interactions with both the flap and with the S2' pocket.

  • Organizational Affiliation

    Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@spcorp.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
390Homo sapiensMutation(s): 0 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 316

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

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
C4 H6 O6
Binding Affinity Annotations 
IDSourceBinding Affinity
316 BindingDB:  3CIC Ki: 3 (nM) from 1 assay(s)
IC50: min: 3, max: 300 (nM) from 2 assay(s)
PDBBind:  3CIC IC50: 3 (nM) from 1 assay(s)
Binding MOAD:  3CIC IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.403α = 90
b = 89.042β = 90
c = 130.698γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description