4TPP

2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Synthesis and preliminary biological evaluation of potent and selective 2-(3-alkoxy-1-azetidinyl) quinolines as novel PDE10A inhibitors with improved solubility.

Rzasa, R.M.Frohn, M.J.Andrews, K.L.Chmait, S.Chen, N.Clarine, J.G.Davis, C.Eastwood, H.A.Horne, D.B.Hu, E.Jones, A.D.Kaller, M.R.Kunz, R.K.Miller, S.Monenschein, H.Nguyen, T.Pickrell, A.J.Porter, A.Reichelt, A.Zhao, X.Treanor, J.J.Allen, J.R.

(2014) Bioorg Med Chem 22: 6570-6585

  • DOI: https://doi.org/10.1016/j.bmc.2014.10.013
  • Primary Citation of Related Structures:  
    4TPM, 4TPP

  • PubMed Abstract: 

    We report the discovery of a novel series of 2-(3-alkoxy-1-azetidinyl) quinolines as potent and selective PDE10A inhibitors. Structure-activity studies improved the solubility (pH 7.4) and maintained high PDE10A activity compared to initial lead compound 3, with select compounds demonstrating good oral bioavailability. X-ray crystallographic studies revealed two distinct binding modes to the catalytic site of the PDE10A enzyme. An ex vivo receptor occupancy assay in rats demonstrated that this series of compounds covered the target within the striatum.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320-1799, USA. Electronic address: rrzasa@amgen.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
351Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
PHAROS:  Q9Y233
GTEx:  ENSG00000112541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y233
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
35D
Query on 35D

Download Ideal Coordinates CCD File 
M [auth A],
T [auth B]
1-[4-(3-{[1-(quinolin-2-yl)azetidin-3-yl]oxy}quinoxalin-2-yl)piperidin-1-yl]ethanone
C27 H27 N5 O2
VSJCZYGHEFDAJZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
N [auth B],
O [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
35D BindingDB:  4TPP IC50: min: 2.6, max: 2.9 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 253.216α = 90
b = 253.216β = 90
c = 253.216γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-12-17 
  • Deposition Author(s): Chmait, S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Data collection
  • Version 1.2: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations