Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49

Experimental Data Snapshot

  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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Design and Synthesis of Selective Phosphodiesterase 4D (PDE4D) Allosteric Inhibitors for the Treatment of Fragile X Syndrome and Other Brain Disorders.

Gurney, M.E.Nugent, R.A.Mo, X.Sindac, J.A.Hagen, T.J.Fox III, D.O'Donnell, J.M.Zhang, C.Xu, Y.Zhang, H.T.Groppi, V.E.Bailie, M.White, R.E.Romero, D.L.Vellekoop, A.S.Walker, J.R.Surman, M.D.Zhu, L.Campbell, R.F.

(2019) J Med Chem 62: 4884-4901

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00193
  • Primary Citation of Related Structures:  
    6NJH, 6NJI, 6NJJ

  • PubMed Abstract: 

    Novel pyridine- and pyrimidine-based allosteric inhibitors are reported that achieve PDE4D subtype selectivity through recognition of a single amino acid difference on a key regulatory domain, known as UCR2, that opens and closes over the catalytic site for cAMP hydrolysis. The design and optimization of lead compounds was based on iterative analysis of X-ray crystal structures combined with metabolite identification. Selectivity for the activated, dimeric form of PDE4D provided potent memory enhancing effects in a mouse model of novel object recognition with improved tolerability and reduced vascular toxicity over earlier PDE4 inhibitors that lack subtype selectivity. The lead compound, 28 (BPN14770), has entered midstage, human phase 2 clinical trials for the treatment of Fragile X Syndrome.

  • Organizational Affiliation

    Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences , University at Buffalo, The State University of New York , Buffalo , New York 14214-8033 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D
A, B
370Homo sapiensMutation(s): 2 
Gene Names: PDE4DDPDE3
UniProt & NIH Common Fund Data Resources
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
PHAROS:  Q08499
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08499
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.45 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.04α = 90
b = 85.66β = 110.41
c = 83.45γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS078034

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence