Crystal structure of PDE5A in complex with a novel inhibitor

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Pharmacokinetics-Driven Optimization of 4(3 H)-Pyrimidinones as Phosphodiesterase Type 5 Inhibitors Leading to TPN171, a Clinical Candidate for the Treatment of Pulmonary Arterial Hypertension.

Wang, Z.Jiang, X.Zhang, X.Tian, G.Yang, R.Wu, J.Zou, X.Liu, Z.Yang, X.Wu, C.Shi, J.Li, J.Suo, J.Wang, Y.Zhang, R.Xu, Z.Gong, X.He, Y.Zhu, W.Aisa, H.A.Jiang, H.Xu, Y.Shen, J.

(2019) J Med Chem 62: 4979-4990

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00123
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Phosphodiesterase type 5 (PDE5) inhibitors are first-line therapy for pulmonary arterial hypertension (PAH) and erectile dysfunction. As a continuing work to improve the terminal half-lives and oral bioavailabilities of our previously reported 4(3 H)-pyrimidones, a pharmacokinetics-driven optimization focusing on the terminal substituent is described. Two major congeneric series of 4(3 H)-pyrimidones, the aminosulfonylphenylpyrimidones and acylaminophenylpyrimidones, were designed, synthesized, and pharmacologically assessed in vitro and in vivo. Among them, compound 15 (TPN171) with subnanomolar potency for PDE5 and good selectivity over PDE6 was finally recognized as a potential drug candidate, and its pharmacokinetic profiles in rats and dogs are significantly improved compared to the starting compound (3). Moreover, TPN171 was proven to exert a longer lasting effect than sildenafil in animal models, providing a foundation for a once-daily oral administration for its clinical use. TPN171 is currently being investigated in a phase II clinical trial for the treatment of PAH.

  • Organizational Affiliation

    CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-specific 3',5'-cyclic phosphodiesterase347Homo sapiensMutation(s): 0 
Gene Names: PDE5APDE5
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens)
Explore O76074 
Go to UniProtKB:  O76074
PHAROS:  O76074
GTEx:  ENSG00000138735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76074
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B0C

Download Ideal Coordinates CCD File 
D [auth A]N-[3-(4,5-diethyl-6-oxo-1,6-dihydropyrimidin-2-yl)-4-propoxyphenyl]-2-(4-methylpiperazin-1-yl)acetamide
C24 H35 N5 O3
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.748α = 90
b = 74.748β = 90
c = 132.02γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references