4KP6

Crystal structure of human phosphodiesterase 4B (PDE4B) in complex with a [1,3,5]triazine derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of triazines as potent, selective and orally active PDE4 inhibitors.

Gewald, R.Grunwald, C.Egerland, U.

(2013) Bioorg.Med.Chem.Lett. 23: 4308-4314

  • DOI: 10.1016/j.bmcl.2013.05.099

  • PubMed Abstract: 
  • Expanding on HTS hit 4 afforded a series of [1,3,5]triazine derivatives as novel PDE4 inhibitors. The SAR development and optimization process with the emphasis on ligand efficiency and physicochemical properties led to the discovery of compound 44 a ...

    Expanding on HTS hit 4 afforded a series of [1,3,5]triazine derivatives as novel PDE4 inhibitors. The SAR development and optimization process with the emphasis on ligand efficiency and physicochemical properties led to the discovery of compound 44 as a potent, selective and orally active PDE4 inhibitor.


    Organizational Affiliation

    BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany. rainer.gewald@telecolumbus.net




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A
340Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
1S1
Query on 1S1

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Download CCD File 
A
2-ethyl-2-{[4-(methylamino)-6-(1H-1,2,4-triazol-1-yl)-1,3,5-triazin-2-yl]amino}butanenitrile
C12 H17 N9
AQTLNSKLZWRJEV-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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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1S1IC50: 0.87 nM BINDINGMOAD
1S1IC50: 0.81 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.168 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 53.332α = 90.00
b = 53.332β = 90.00
c = 229.048γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description