3SIE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1021/jm200644r
  • Primary Citation of Related Structures:  

  • 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 bioacti ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-specific 3',5'-cyclic phosphodiesterase
A, B
347Homo sapiensMutation(s): 0 
Gene Names: PDE5A (PDE5)
EC: 3.1.4.35
Find proteins for O76074 (Homo sapiens)
Go to Gene View: PDE5A
Go to UniProtKB:  O76074
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5BO
Query on 5BO

Download SDF File 
Download CCD File 
A, B
5-bromo-6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
C20 H27 Br N4 O4 S
QERPGINNBBVVSA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5BOKd: 420 nM (100) BINDINGDB
5BOIC50: 13.3 nM BINDINGMOAD
5BOIC50: 13.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.180α = 90.00
b = 94.120β = 90.00
c = 114.260γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
ADSCdata collection
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2012-06-27
    Type: Experimental preparation