Catalytic Domain Of Human Phosphodiesterase 4B In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design

Card, G.L.Blasdel, L.England, B.P.Zhang, C.Suzuki, Y.Gillette, S.Fong, D.Ibrahim, P.N.Artis, D.R.Bollag, G.Milburn, M.V.Kim, S.-H.Schlessinger, J.Zhang, K.Y.J.

(2005) Nat Biotechnol 23: 201-207

  • DOI: https://doi.org/10.1038/nbt1059
  • Primary Citation of Related Structures:  
    1Y2B, 1Y2C, 1Y2D, 1Y2E, 1Y2H, 1Y2J, 1Y2K

  • PubMed Abstract: 

    Cyclic nucleotide phosphodiesterases (PDEs) comprise a large family of enzymes that regulate a variety of cellular processes. We describe a family of potent PDE4 inhibitors discovered using an efficient method for scaffold-based drug design. This method involves an iterative approach starting with low-affinity screening of compounds followed by high-throughput cocrystallography to reveal the molecular basis underlying the activity of the newly identified compounds. Through detailed structural analysis of the interaction of the initially discovered pyrazole carboxylic ester scaffold with PDE4D using X-ray crystallography, we identified three sites of chemical substitution and designed small selective libraries of scaffold derivatives with modifications at these sites. A 4,000-fold increase in the potency of this PDE4 inhibitor was achieved after only two rounds of chemical synthesis and the structural analysis of seven pyrazole derivatives bound to PDE4B or PDE4D, revealing the robustness of this approach for identifying new inhibitors that can be further developed into drug candidates.

  • Organizational Affiliation

    Plexxikon Inc., 91 Bolivar Dr., Berkeley, California 94710, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
A, B
398Homo sapiensMutation(s): 1 
Gene Names: PDE4B
UniProt & NIH Common Fund Data Resources
Find proteins for Q07343 (Homo sapiens)
Explore Q07343 
Go to UniProtKB:  Q07343
PHAROS:  Q07343
GTEx:  ENSG00000184588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07343
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CME
A, B
Binding Affinity Annotations 
IDSourceBinding Affinity
7DE BindingDB:  1Y2J IC50: min: 33, max: 33 (nM) from 2 assay(s)
PDBBind:  1Y2J IC50: 33 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.484α = 90
b = 94.235β = 90
c = 106.843γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
ELVESdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance