3G45

Crystal structure of human phosphodiesterase 4b with regulatory domain and d155988

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.

Burgin, A.B., Magnusson, O.T., Singh, J., Witte, P., Staker, B.L., Bjornsson, J.M., Thorsteinsdottir, M., Hrafnsdottir, S., Hagen, T., Kiselyov, A.S., Stewart, L.J., Gurney, M.E.

(2010) Nat Biotechnol 28: 63-70

  • DOI: 10.1038/nbt.1598
  • Primary Citation of Related Structures:  
    3G45, 3IAD, 3G58, 3G4I, 3G4K, 3G4L, 3G4G

  • PubMed Abstract: 

    • Phosphodiesterase 4 (PDE4), the primary cAMP-hydrolyzing enzyme in cells, is a promising drug target for a wide range of conditions. Here we present seven co-crystal structures of PDE4 and bound inhibitors that show the regulatory domain closed across the active site, thereby revealing the structural basis of PDE4 regulation ...

    Phosphodiesterase 4 (PDE4), the primary cAMP-hydrolyzing enzyme in cells, is a promising drug target for a wide range of conditions. Here we present seven co-crystal structures of PDE4 and bound inhibitors that show the regulatory domain closed across the active site, thereby revealing the structural basis of PDE4 regulation. This structural insight, together with supporting mutagenesis and kinetic studies, allowed us to design small-molecule allosteric modulators of PDE4D that do not completely inhibit enzymatic activity (I(max) approximately 80-90%). These allosteric modulators have reduced potential to cause emesis, a dose-limiting side effect of existing active site-directed PDE4 inhibitors, while maintaining biological activity in cellular and in vivo models. Our results may facilitate the design of CNS therapeutics modulating cAMP signaling for the treatment of Alzheimer's disease, Huntington's disease, schizophrenia and depression, where brain distribution is desired for therapeutic benefit.

    Organizational Affiliation: 

    deCODE biostructures, Bainbridge Island, Washington, USA. aburgin@embios.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B A, B421Homo sapiensMutation(s): 0 
Gene Names: PDE4B, DPDE4
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
NIH Common Fund Data Resources
PHAROS:  Q07343
GTEx:  ENSG00000184588
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
988
Query on 988
Download Ideal Coordinates CCD File 
A, B
8-(3-nitrophenyl)-6-(pyridin-4-ylmethyl)quinoline
C21 H15 N3 O2
XRSKAWJXBDACRF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
988IC50 :  4.400000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.004α = 90
b = 95.004β = 90
c = 93.714γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-02-03 
  • Released Date: 2010-01-19 
    • Deposition Author(s): Staker, B.L.

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy