Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

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This is version 1.2 of the entry. See complete history


Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors.

Xu, Z.Liu, Z.Chen, T.Chen, T.T.Wang, Z.Tian, G.Shi, J.Wang, X.Lu, Y.Yan, X.Wang, G.Jiang, H.Chen, K.Wang, S.Xu, Y.Shen, J.Zhu, W.

(2011) J Med Chem 54: 5607-5611

  • DOI: https://doi.org/10.1021/jm200644r
  • Primary Citation of Related Structures:  
    3SHY, 3SHZ, 3SIE

  • PubMed Abstract: 

    For proof-of-concept of halogen bonding in drug design, a series of halogenated compounds were designed based on a lead structure as new inhibitors of phosphodiesterase type 5. Bioassay results revealed a good correlation between the measured bioactivity and the calculated halogen bond energy. Our X-ray crystal structures verified the existence of the predicted halogen bonds, demonstrating that the halogen bond is an applicable tool in drug design and should be routinely considered in lead optimization.

  • Organizational Affiliation

    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 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: PDE5PDE5A
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
Binding Affinity Annotations 
IDSourceBinding Affinity
5FO BindingDB:  3SHY Kd: 1700 (nM) from 1 assay(s)
PDBBind:  3SHY IC50: 90.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.458α = 90
b = 74.458β = 90
c = 131.926γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata 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: 2011-08-24
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations