phosphodiesterase-9A in complex with inhibitor WYQ-C36D

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.241 

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Discovery of a Phosphodiesterase 9A Inhibitor as a Potential Hypoglycemic Agent.

Shao, Y.X.Huang, M.Cui, W.Feng, L.J.Wu, Y.Cai, Y.Li, Z.Zhu, X.Liu, P.Wan, Y.Ke, H.Luo, H.B.

(2014) J Med Chem 57: 10304-10313

  • DOI: https://doi.org/10.1021/jm500836h
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphodiesterase 9 (PDE9) inhibitors have been studied as potential therapeutics for treatment of diabetes and Alzheimer's disease. Here we report a potent PDE9 inhibitor 3r that has an IC50 of 0.6 nM and >150-fold selectivity over other PDEs. The HepG2 cell-based assay shows that 3r inhibits the mRNA expression of phosphoenolpyruvate carboxykinase and glucose 6-phosphatase. These activities of 3r, together with the reasonable pharmacokinetic properties and no acute toxicity at 1200 mg/kg dosage, suggest its potential as a hypoglycemic agent. The crystal structure of PDE9-3r reveals significantly different conformation and hydrogen bonding pattern of 3r from those of previously published 28s. Both 3r and 28s form a hydrogen bond with Tyr424, a unique PDE9 residue (except for PDE8), but 3r shows an additional hydrogen bond with Ala452. This structure information might be useful for design of PDE9 inhibitors.

  • Organizational Affiliation

    School of Pharmaceutical Sciences, Sun Yat-Sen University , Guangzhou 510006, P. R. China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphodiesterase 9A
A, B
533Pan troglodytesMutation(s): 0 
Gene Names: PDE9A
Find proteins for H2QL32 (Pan troglodytes)
Explore H2QL32 
Go to UniProtKB:  H2QL32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2QL32
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.58α = 90
b = 103.58β = 90
c = 268.657γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references