3CID

Structure of BACE Bound to SCH726222


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1AB390Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
NIH Common Fund Data Resources
PHAROS  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
318
Query on 318

Download CCD File 
A, B
N'-[(1S,2S)-2-[(4S)-1-benzyl-5-oxoimidazolidin-4-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
C34 H40 F2 N4 O4
HZWNNIVRFLRAQW-CHQNGUEUSA-N
 Ligand Interaction
TAR
Query on TAR

Download CCD File 
A, B
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
318IC50:  5   nM  BindingDB
318IC50:  1100   nM  BindingDB
318IC50:  5   nM  Binding MOAD
318IC50 :  5   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.296α = 90
b = 89.131β = 90
c = 130.59γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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