3O57

Catalytic domain of human phosphodiesterase 4b2b in complex with a 5-heterocycle pyrazolopyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3O57/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-07-28 Released: 2011-08-03 
• Deposition Author(s): Somers, D.O., Neu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Pyrazolopyridines as potent PDE4B inhibitors: 5-heterocycle SAR.

Mitchell, C.J., Ballantine, S.P., Coe, D.M., Cook, C.M., Delves, C.J., Dowle, M.D., Edlin, C.D., Hamblin, J.N., Holman, S., Johnson, M.R., Jones, P.S., Keeling, S.E., Kranz, M., Lindvall, M., Lucas, F.S., Neu, M., Solanke, Y.E., Somers, D.O., Trivedi, N.A., Wiseman, J.O.

(2010) Bioorg Med Chem Lett 20: 5803-5806

• PubMed: 20732811 
• DOI: https://doi.org/10.1016/j.bmcl.2010.07.136
• Primary Citation of Related Structures:  
  3O56, 3O57


• PubMed Abstract: 
  

  Following the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective phosphodiesterase 4B inhibitors, [Hamblin, J. N.; Angell, T.; Ballentine, S., et al. Bioorg. Med. Chem. Lett.2008, 18, 4237] the SAR of the 5-position was investigated further. A range of substituted heterocycles showed good potencies against PDE4. Optimisation using X-ray crystallography and computational modelling led to the discovery of 16, with sub-nM inhibition of LPS-induced TNF-α production from isolated human peripheral blood mononuclear cells.

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Organizational Affiliation: 

GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.51 kDa 
• Atom Count: 3,069 
• Modelled Residue Count: 336 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	353	Homo sapiens	Mutation(s): 3  Gene Names: PDE4B, DPDE4 EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens) Go to UniProtKB:  Q07343
PHAROS:  Q07343 GTEx:  ENSG00000184588

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZG2	G [auth A]	5-[5-benzyl-4-(2-oxo-2-pyrrolidin-1-ylethyl)-1,3-oxazol-2-yl]-1-ethyl-N-(tetrahydro-2H-pyran-4-yl)-1H-pyrazolo[3,4-b]pyridin-4-amine C29 H34 N6 O3 XOLUUYCIKUMYDW-UHFFFAOYSA-N
GOL	H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ARS	D [auth A], E [auth A], F [auth A]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZG2	PDBBind:  3O57	IC50: 0.08 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.240 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.622	α = 90
b = 94.907	β = 90
c = 105.853	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Somers, D.O., Neu, M.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description