3QPO

Structure of PDE10-inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Use of Structure-Based Design to Discover a Potent, Selective, In Vivo Active Phosphodiesterase 10A Inhibitor Lead Series for the Treatment of Schizophrenia.

Helal, C.J.Kang, Z.Hou, X.Pandit, J.Chappie, T.A.Humphrey, J.M.Marr, E.S.Fennell, K.F.Chenard, L.K.Fox, C.Schmidt, C.J.Williams, R.D.Chapin, D.S.Siuciak, J.Lebel, L.Menniti, F.Cianfrogna, J.Fonseca, K.R.Nelson, F.R.O'Connor, R.Macdougall, M.McDowell, L.Liras, S.

(2011) J Med Chem 54: 4536-4547

  • DOI: 10.1021/jm2001508
  • Primary Citation of Related Structures:  
    3QPN, 3QPO, 3QPP

  • PubMed Abstract: 
  • Utilizing structure-based virtual library design and scoring, a novel chimeric series of phosphodiesterase 10A (PDE10A) inhibitors was discovered by synergizing binding site interactions and ADME properties of two chemotypes. Virtual libraries were docked and scored for potential binding ability, followed by visual inspection to prioritize analogs for parallel and directed synthesis ...

    Utilizing structure-based virtual library design and scoring, a novel chimeric series of phosphodiesterase 10A (PDE10A) inhibitors was discovered by synergizing binding site interactions and ADME properties of two chemotypes. Virtual libraries were docked and scored for potential binding ability, followed by visual inspection to prioritize analogs for parallel and directed synthesis. The process yielded highly potent and selective compounds such as 16. New X-ray cocrystal structures enabled rational design of substituents that resulted in the successful optimization of physical properties to produce in vivo activity and to modulate microsomal clearance and permeability.


    Organizational Affiliation

    Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States. chris.j.helal@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A A362Rattus norvegicusMutation(s): 0 
Gene Names: Pde10a
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
Find proteins for Q9QYJ6 (Rattus norvegicus)
Explore Q9QYJ6 
Go to UniProtKB:  Q9QYJ6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PFR
Query on PFR

Download Ideal Coordinates CCD File 
A
7-methoxy-4-[(3S)-3-phenylpiperidin-1-yl]-6-[2-(pyridin-2-yl)ethoxy]quinazoline
C27 H28 N4 O2
DWBBOQWADWMQGE-OAQYLSRUSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PFRIC50:  247   nM  BindingDB
PFRIC50 :  247   nM  PDBBind
PFRIC50:  247   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.451α = 90
b = 120.451β = 90
c = 82.061γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-02-14 
  • Released Date: 2011-06-15 
  • Deposition Author(s): Pandit, J., Marr, E.S.

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references