2QYN

Crystal structure of PDE4D2 in complex with inhibitor NPV

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors.

Wang, H., Peng, M.S., Chen, Y., Geng, J., Robinson, H., Houslay, M.D., Cai, J., Ke, H.

(2007) Biochem J 408: 193-201

  • DOI: 10.1042/BJ20070970
  • Primary Citation of Related Structures:  
    2QYN, 2QYM, 2QYL, 2QYK

  • PubMed Abstract: 

    • PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible ...

    PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP {4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid} as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7260, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-specific 3',5'-cyclic phosphodiesterase 4D A, B328Homo sapiensMutation(s): 0 
Gene Names: PDE4D, DPDE3
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.53 (UniProt)
Find proteins for Q08499 (Homo sapiens)
Explore Q08499 
Go to UniProtKB:  Q08499
NIH Common Fund Data Resources
PHAROS:  Q08499
GTEx:  ENSG00000113448
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NPV
Query on NPV
Download Ideal Coordinates CCD File 
A, B
4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid
C21 H13 N3 O4
QTNUWEKKZHSUQO-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NPVIC50:  570   nM  Binding MOAD
NPVIC50 :  570   nM  PDBBind
NPVIC50:  1   nM  BindingDB
NPVIC50:  68   nM  BindingDB
NPVIC50:  0.6000000238418579   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.1α = 90
b = 80.626β = 90
c = 163.315γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2007-08-15 
  • Released Date: 2008-04-08 
    • Deposition Author(s): Ke, H.

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance