4OEW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Thermodynamic and structural characterization of halogen bonding in protein-ligand interactions: a case study of PDE5 and its inhibitors.

Ren, J.He, Y.Chen, W.Chen, T.Wang, G.Wang, Z.Xu, Z.Luo, X.Zhu, W.Jiang, H.Shen, J.Xu, Y.

(2014) J.Med.Chem. 57: 3588-3593

  • DOI: 10.1021/jm5002315
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reve ...

    The significance of halogen bonding in protein-ligand interactions has been recognized recently. We present here the first comprehensive thermodynamic and structural characterization of halogen bonding in PDE5-inhibitor interactions. ITC studies reveal that binding strength of the halogen bonding between chlorine, bromine, and iodine of inhibitor and the protein is -1.57, -3.09, and -5.59 kJ/mol, respectively. The halogens interact with the designed residue Y612 and an unexpected buried water molecule.


    Organizational Affiliation

    CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS) , 555 Zuchongzhi Road, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-specific 3',5'-cyclic phosphodiesterase
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5IO
Query on 5IO

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Download CCD File 
A
6-ethyl-5-iodo-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
C20 H27 I N4 O4 S
CLYYLXSJJMHCHN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5IOKd: 150 nM (100) BINDINGDB
5IOKd: 1450 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 74.120α = 90.00
b = 74.120β = 90.00
c = 131.800γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release