4KP6

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

• PDB DOI: https://doi.org/10.2210/pdb4KP6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-13 Released: 2013-07-10 
• Deposition Author(s): Gewald, R., Grunwald, C., Egerland, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 

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

• PubMed: 23806553 
• DOI: https://doi.org/10.1016/j.bmcl.2013.05.099
• Primary Citation of Related Structures:  
  4KP6


• 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 as a potent, selective and orally active PDE4 inhibitor.

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Organizational Affiliation: 

BioCrea GmbH, Meissner Strasse 191, 01445 Radebeul, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.59 kDa 
• Atom Count: 2,933 
• Modelled Residue Count: 324 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	340	Homo sapiens	Mutation(s): 0  Gene Names: DPDE4, PDE4B EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens) Explore Q07343  Go to UniProtKB:  Q07343
PHAROS:  Q07343 GTEx:  ENSG00000184588

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1S1	B [auth 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
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1S1	PDBBind:  4KP6	IC50: 0.81 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.198 
• R-Value Work: 0.168 
• R-Value Observed: 0.169 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.332	α = 90
b = 53.332	β = 90
c = 229.048	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Gewald, R., Grunwald, C., Egerland, U.

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description
• Version 1.3: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations