3D3P

Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.3 of the entry. See complete history. 


Literature

Pyrazolopyridines as a novel structural class of potent and selective PDE4 inhibitors.

Hamblin, J.N., Angell, T.D., Ballantine, S.P., Cook, C.M., Cooper, A.W., Dawson, J., Delves, C.J., Jones, P.S., Lindvall, M., Lucas, F.S., Mitchell, C.J., Neu, M.Y., Ranshaw, L.E., Solanke, Y.E., Somers, D.O., Wiseman, J.O.

(2008) Bioorg Med Chem Lett 18: 4237-4241

  • DOI: https://doi.org/10.1016/j.bmcl.2008.05.052
  • Primary Citation of Related Structures:  
    3D3P

  • PubMed Abstract: 

    • Optimisation of a high-throughput screening hit resulted in the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective inhibitors of Phosphodiesterase 4 (PDE4). Herein, we describe early SAR studies around this novel template highlighting preferred substituents and rationalization of SAR through X-ray crystal structures of analogues bound to the PDE4 active site ...

    Optimisation of a high-throughput screening hit resulted in the discovery of 4-(substituted amino)-1-alkyl-pyrazolo[3,4-b]pyridine-5-carboxamides as potent and selective inhibitors of Phosphodiesterase 4 (PDE4). Herein, we describe early SAR studies around this novel template highlighting preferred substituents and rationalization of SAR through X-ray crystal structures of analogues bound to the PDE4 active site. Pyrazolopyridine 20a was found to be a potent and selective PDE4 inhibitor which also inhibits LPS induced TNF-alpha production from isolated human peripheral blood mononuclear cells and has an encouraging rat PK profile suitable for oral dosing.

    Organizational Affiliation: 

    GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. nicole.j.hamblin@gsk.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4BA353Homo sapiensMutation(s): 3 
Gene Names: PDE4B, DPDE4
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
20A
Query on 20A
Download Ideal Coordinates CCD File 
D [auth A]1-ethyl-N-(phenylmethyl)-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide
C21 H25 N5 O2
QZGJNFBMYYEFGM-UHFFFAOYSA-N		 Ligand Interaction
ARS
Query on ARS
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]		ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
20A PDBBind:  3D3P IC50: 3.16 (nM) from 1 assay(s)
Binding MOAD:  3D3P IC50: 3.1 (nM) from 1 assay(s)
BindingDB:  3D3P IC50: 3.16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.448α = 90
b = 94.725β = 90
c = 105.671γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations