6A3N

Crystal structure of the PDE9 catalytic domain in complex with inhibitor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent, Selective, and Orally Bioavailable Inhibitors against Phosphodiesterase-9, a Novel Target for the Treatment of Vascular Dementia.

Wu, Y.Zhou, Q.Zhang, T.Li, Z.Chen, Y.P.Zhang, P.Yu, Y.F.Geng, H.Tian, Y.J.Zhang, C.Wang, Y.Chen, J.W.Chen, Y.Luo, H.B.

(2019) J Med Chem 62: 4218-4224

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b01041
  • Primary Citation of Related Structures:  
    6A3N

  • PubMed Abstract: 

    To identify phosphodiesterase-9 (PDE9) as a novel target for the treatment of vascular dementia (VaD), a series of pyrazolopyrimidinone analogues were discovered based on a hit 1. Hit-to-lead optimization resulted in a potent inhibitor 2 with excellent selectivity and physicochemical properties to enable in vivo studies. Oral administration of 2 (5.0 mg/kg) caused notable therapeutic effects in the VaD mouse model, providing a promising lead or chemical probe for investigating the biological functions of PDE9 inhibition.


  • 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
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
322Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.249 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.11α = 90
b = 104.11β = 90
c = 269.079γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China81522041 and 21572279

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description