4PZX

Synthesis, Characterization and PK/PD Studies of a Series of Spirocyclic Pyranochromene BACE1 Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis, characterization, and PK/PD studies of a series of spirocyclic pyranochromene BACE1 inhibitors.

Volgraf, M.Chan, L.Huestis, M.P.Purkey, H.E.Burkard, M.Geck Do, M.Harris, J.Hunt, K.W.Liu, X.Lyssikatos, J.P.Rana, S.Thomas, A.A.Vigers, G.P.Siu, M.

(2014) Bioorg Med Chem Lett 24: 2477-2480

  • DOI: https://doi.org/10.1016/j.bmcl.2014.04.012
  • Primary Citation of Related Structures:  
    4PZW, 4PZX

  • PubMed Abstract: 

    The development of 1,3,4,4a,5,10a-hexahydropyrano[3,4-b]chromene analogs as BACE1 inhibitors is described. Introduction of the spirocyclic pyranochromene scaffold yielded several advantages over previous generation cores, including increased potency, reduced efflux, and reduced CYP2D6 inhibition. Compound 13 (BACE1 IC50=110 nM) demonstrated a reduction in CSF Aβ in wild type rats after a single dose.


  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: volgrafm@gene.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1406Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2X5
Query on 2X5

Download Ideal Coordinates CCD File 
C [auth A](4R,4a'R,10a'R)-7'-(5-chloropyridin-3-yl)-3',4',4a',10a'-tetrahydro-1'H-spiro[1,3-oxazole-4,5'-pyrano[3,4-b]chromen]-2-amine
C19 H18 Cl N3 O3
BGRWOLNAPSRJIS-UCLAIMLFSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
2X5 Binding MOAD:  4PZX IC50: 1000 (nM) from 1 assay(s)
BindingDB:  4PZX IC50: min: 130, max: 1000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.2α = 90
b = 103.55β = 90
c = 99.51γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2014-10-15
    Changes: Structure summary