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

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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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 phosphodiesterase
A, B
347Homo 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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5BO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C20 H27 Br N4 O4 S
Binding Affinity Annotations 
IDSourceBinding Affinity
5BO BindingDB:  3SIE Kd: 420 (nM) from 1 assay(s)
PDBBind:  3SIE IC50: 13.3 (nM) from 1 assay(s)
Binding MOAD:  3SIE IC50: 13.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.18α = 90
b = 94.12β = 90
c = 114.26γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report

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: 2012-06-27
    Changes: Experimental preparation
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations