6UVV | pdb_00006uvv

BACE-1 in complex with compound #17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.186 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.141 (Depositor) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UVV

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Preparation and biological evaluation of BACE1 inhibitors: Leveraging trans-cyclopropyl moieties as ligand efficient conformational constraints.

Winneroski, L.L.Erickson, J.A.Green, S.J.Lopez, J.E.Stout, S.L.Porter, W.J.Timm, D.E.Audia, J.E.Barberis, M.Beck, J.P.Boggs, L.N.Borders, A.R.Boyer, R.D.Brier, R.A.Hembre, E.J.Hendle, J.Garcia-Losada, P.Minguez, J.M.Mathes, B.M.May, P.C.Monk, S.A.Rankovic, Z.Shi, Y.Watson, B.M.Yang, Z.Mergott, D.J.

(2020) Bioorg Med Chem 28: 115194-115194

  • DOI: https://doi.org/10.1016/j.bmc.2019.115194
  • Primary Citation Related Structures: 
    6UVP, 6UVV, 6UVY, 6UWP, 6UWV

  • PubMed Abstract: 

    Inhibition of BACE1 has become an important strategy in the quest for disease modifying agents to slow the progression of Alzheimer's disease. We previously reported the fragment-based discovery of LY2811376, the first BACE1 inhibitor reported to demonstrate robust reduction of human CSF Aβ in a Phase I clinical trial. We also reported on the discovery of LY2886721, a potent BACE1 inhibitor that reached phase 2 clinical trials. Herein we describe the preparation and structure activity relationships (SAR) of a series of BACE1 inhibitors utilizing trans-cyclopropyl moieties as conformational constraints. The design, details of the stereochemically complex organic synthesis, and biological activity of these BACE1 inhibitors is described.


  • Organizational Affiliation
    • Lilly Research Laboratories, A Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.

Macromolecule Content 

  • Total Structure Weight: 99.38 kDa 
  • Atom Count: 7,555 
  • Modeled Residue Count: 782 
  • Deposited Residue Count: 884 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
442Homo 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QJV
(Subject of Investigation/LOI)

Query on QJV



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
(1R,2R)-2-[(4aS,7aR)-2-amino-4a,5-dihydro-4H-furo[3,4-d][1,3]thiazin-7a(7H)-yl]-N-butylcyclopropane-1-carboxamide
C14 H23 N3 O2 S
WVAFMFLAAGBATC-OXIWPEFWSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
H [auth B]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QJV BindingDB:  6UVV IC50: 6640 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.186 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.141 (Depositor) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.288α = 90
b = 90.043β = 90
c = 130.948γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary