2VA7

X-ray crystal structure of beta secretase complexed with compound 27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine Beta-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency.

Edwards, P.D.Albert, J.S.Sylvester, M.Aharony, D.Andisik, D.Callaghan, O.Campbell, J.B.Carr, R.A.Chessari, G.Congreve, M.Frederickson, M.Folmer, R.H.A.Geschwindner, S.Koether, G.Kolmodin, K.Krumrine, J.Mauger, R.C.Murray, C.W.Olsson, L.L.Patel, S.Spear, N.Tian, G.

(2007) J.Med.Chem. 50: 5912

  • DOI: 10.1021/jm070829p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screeni ...

    Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screening. Structure-guided evolution of these fragments using X-ray crystallography together with potency determination using surface plasmon resonance and functional enzyme inhibition assays afforded micromolar inhibitors. Similarity searching around the isocytosine core led to the identification of a related series of inhibitors, the dihydroisocytosines. By leveraging the knowledge of the ligand-BACE-1 recognition features generated from the isocytosines, the dihydroisocytosines were efficiently optimized to submicromolar potency. Compound 29, with an IC50 of 80 nM, a ligand efficiency of 0.37, and cellular activity of 470 nM, emerged as the lead structure for future optimization.


    Organizational Affiliation

    CNS Discovery Research, AstraZeneca Pharmaceuticals LP, 1800 Concord Pike, Wilmington, DE 19850-5437, USA. philip.edwards@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-SECRETASE 1 .
A
455Homo sapiensMutations: K58R, K59R
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
C27
Query on C27

Download SDF File 
Download CCD File 
A
(6R)-2-amino-6-[2-(3'-methoxybiphenyl-3-yl)ethyl]-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
C21 H25 N3 O2
VDFBMQAUECXNKR-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C27IC50: 80 - 470 nM (99) BINDINGDB
C27IC50: 640 nM BINDINGMOAD
C27IC50: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.687α = 90.00
b = 102.687β = 90.00
c = 168.340γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
C-SEARCHphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance