3CIB

Structure of BACE Bound to SCH727596


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 crafted to achieve interactions with both the flap and with the S2' pocket ...

    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 1A, B390Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
314 (Subject of Investigation/LOI)
Query on 314

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]N'-[(1S,2R)-2-[(2R,4S)-4-benzylpiperidin-2-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
C36 H45 F2 N3 O3
UKXYKYZOSFWZIM-FLQGXGFZSA-N
 Ligand Interaction
TAR
Query on TAR

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
314 BindingDB:  3CIB IC50: min: 14, max: 522 (nM) from 2 assay(s)
PDBBind:  3CIB IC50: 14 (nM) from 1 assay(s)
Binding MOAD:  3CIB IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.677α = 90
b = 89.435β = 90
c = 131.446γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
CNSphasing

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