4MYQ

Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for the design of selective phosphodiesterase 4B inhibitors.

Fox, D.Burgin, A.B.Gurney, M.E.

(2014) Cell Signal 26: 657-663

  • DOI: 10.1016/j.cellsig.2013.12.003

  • PubMed Abstract: 
  • Phosphodiesterase-4B (PDE4B) regulates the pro-inflammatory Toll Receptor -Tumor Necrosis Factor α (TNFα) pathway in monocytes, macrophages and microglial cells. As such, it is an important, although under-exploited molecular target for anti-inflamma ...

    Phosphodiesterase-4B (PDE4B) regulates the pro-inflammatory Toll Receptor -Tumor Necrosis Factor α (TNFα) pathway in monocytes, macrophages and microglial cells. As such, it is an important, although under-exploited molecular target for anti-inflammatory drugs. This is due in part to the difficulty of developing selective PDE4B inhibitors as the amino acid sequence of the PDE4 active site is identical in all PDE4 subtypes (PDE4A-D). We show that highly selective PDE4B inhibitors can be designed by exploiting sequence differences outside the active site. Specifically, PDE4B selectivity can be achieved by capture of a C-terminal regulatory helix, now termed CR3 (Control Region 3), across the active site in a conformation that closes access by cAMP. PDE4B selectivity is driven by a single amino acid polymorphism in CR3 (Leu674 in PDE4B1 versus Gln594 in PDE4D). The reciprocal mutations in PDE4B and PDE4D cause a 70-80 fold shift in selectivity. Our structural studies show that CR3 is flexible and can adopt multiple orientations and multiple registries in the closed conformation. The new co-crystal structure with bound ligand provides a guide map for the design of PDE4B selective anti-inflammatory drugs.


    Organizational Affiliation

    Emerald Bio, Bainbridge Island, WA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A
372Homo sapiensMutation(s): 0 
Gene Names: PDE4B (DPDE4)
EC: 3.1.4.53
Find proteins for Q07343 (Homo sapiens)
Go to Gene View: PDE4B
Go to UniProtKB:  Q07343
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
19T
Query on 19T

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Download CCD File 
A
(4-{[2-(5-chlorothiophen-2-yl)-5-ethyl-6-methylpyrimidin-4-yl]amino}phenyl)acetic acid
C19 H18 Cl N3 O2 S
FDVSPBLZPJMXFV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
19TIC50: 1700 - 1997 nM (85) BINDINGDB
19TIC50: 32 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 99.700α = 90.00
b = 99.700β = 90.00
c = 47.020γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-01
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description