4QGE

phosphodiesterase-9A in complex with inhibitor WYQ-C36D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/jm500836h

  • 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 H ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphodiesterase 9A
A, B
533Pan troglodytesMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
Find proteins for H2QL32 (Pan troglodytes)
Go to Gene View: PDE9A
Go to UniProtKB:  H2QL32
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
35O
Query on 35O

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Download CCD File 
A, B
N~2~-(1-cyclopentyl-4-oxo-4,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl)-N-(4-methoxyphenyl)-D-alaninamide
C20 H24 N6 O3
UBBCZBKJYNXHGT-GFCCVEGCSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
35OIC50: 0.6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.580α = 90.00
b = 103.580β = 90.00
c = 268.657γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
ADSCdata collection
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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