4QGE

phosphodiesterase-9A in complex with inhibitor WYQ-C36D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.268 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 35OClick on this verticalbar to view details

This is version 1.3 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: https://doi.org/10.1021/jm500836h
  • Primary Citation of Related Structures:  
    4QGE

  • 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.


Macromolecules
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
EC: 3.1.4.35
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
35O
Query on 35O

Download Ideal Coordinates CCD File 
C [auth A],
F [auth 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
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.268 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.230 (DCC) 
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
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 35OClick on this verticalbar to view details

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
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary