4ZSP

BACE crystal structure with bicyclic aminothiazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Preparation and biological evaluation of conformationally constrained BACE1 inhibitors.

Winneroski, L.L.Schiffler, M.A.Erickson, J.A.May, P.C.Monk, S.A.Timm, D.E.Audia, J.E.Beck, J.P.Boggs, L.N.Borders, A.R.Boyer, R.D.Brier, R.A.Hudziak, K.J.Klimkowski, V.J.Garcia Losada, P.Mathes, B.M.Stout, S.L.Watson, B.M.Mergott, D.J.

(2015) Bioorg Med Chem 23: 3260-3268

  • DOI: 10.1016/j.bmc.2015.04.062
  • Primary Citation of Related Structures:  
    4ZSM, 4ZSP, 4ZSQ, 4ZSR

  • PubMed Abstract: 
  • The BACE1 enzyme is a key target for Alzheimer's disease. During our BACE1 research efforts, fragment screening revealed that bicyclic thiazine 3 had low millimolar activity against BACE1. Analysis of the co-crystal structure of 3 suggested that potency could be increased through extension toward the S3 pocket and through conformational constraint of the thiazine core ...

    The BACE1 enzyme is a key target for Alzheimer's disease. During our BACE1 research efforts, fragment screening revealed that bicyclic thiazine 3 had low millimolar activity against BACE1. Analysis of the co-crystal structure of 3 suggested that potency could be increased through extension toward the S3 pocket and through conformational constraint of the thiazine core. Pursuit of S3-binding groups produced low micromolar inhibitor 6, which informed the S3-design for constrained analogs 7 and 8, themselves prepared via independent, multi-step synthetic routes. Biological characterization of BACE inhibitors 6-8 is described.


    Organizational Affiliation

    Lilly Research Laboratories, A Division of Eli Lilly & Co., Lilly Corporate Center, Indianapolis, IN 46285, USA. Electronic address: mergottdu@lilly.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B442Homo 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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4RZ
Query on 4RZ

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
N-[(4aS,6S,8aR)-2-amino-4a,5,6,7,8,8a-hexahydro-4H-3,1-benzothiazin-6-yl]-3-chlorobenzamide
C15 H18 Cl N3 O S
TUSBLKXHGGIFCU-KGYLQXTDSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
4RZ Binding MOAD:  4ZSP IC50: 1830 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.647α = 90
b = 91.689β = 90
c = 131.205γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2015-05-13 
  • Released Date: 2015-06-10 
  • Deposition Author(s): Timm, D.E.

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references