Human PDE9 in complex with selective compound

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.1 of the entry. See complete history


Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors.

Claffey, M.M.Helal, C.J.Verhoest, P.R.Kang, Z.Fors, K.S.Jung, S.Zhong, J.Bundesmann, M.W.Hou, X.Lui, S.Kleiman, R.J.Vanase-Frawley, M.Schmidt, A.W.Menniti, F.Schmidt, C.J.Hoffman, W.E.Hajos, M.McDowell, L.O'Connor, R.E.Macdougall-Murphy, M.Fonseca, K.R.Becker, S.L.Nelson, F.R.Liras, S.

(2012) J Med Chem 55: 9055-9068

  • DOI: https://doi.org/10.1021/jm3009635
  • Primary Citation of Related Structures:  
    4E90, 4G2J, 4G2L

  • PubMed Abstract: 

    Phosphodiesterase 9A inhibitors have shown activity in preclinical models of cognition with potential application as novel therapies for treating Alzheimer's disease. Our clinical candidate, PF-04447943 (2), demonstrated acceptable CNS permeability in rats with modest asymmetry between central and peripheral compartments (free brain/free plasma = 0.32; CSF/free plasma = 0.19) yet had physicochemical properties outside the range associated with traditional CNS drugs. To address the potential risk of restricted CNS penetration with 2 in human clinical trials, we sought to identify a preclinical candidate with no asymmetry in rat brain penetration and that could advance into development. Merging the medicinal chemistry strategies of structure-based design with parallel chemistry, a novel series of PDE9A inhibitors was identified that showed improved selectivity over PDE1C. Optimization afforded preclinical candidate 19 that demonstrated free brain/free plasma ≥ 1 in rat and reduced microsomal clearance along with the ability to increase cyclic guanosine monophosphosphate levels in rat CSF.

  • Organizational Affiliation

    Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. michelle.m.claffey@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
UniProt & NIH Common Fund Data Resources
Find proteins for O76083 (Homo sapiens)
Explore O76083 
Go to UniProtKB:  O76083
PHAROS:  O76083
GTEx:  ENSG00000160191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76083
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
0WL BindingDB:  4G2L IC50: 32 (nM) from 1 assay(s)
PDBBind:  4G2L IC50: 32 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.226α = 90
b = 104.226β = 90
c = 270.476γ = 90
Software Package:
Software NamePurpose

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2013-05-29 
  • Deposition Author(s): Liu, S.

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-29
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description