5U7L

PDE2 catalytic domain complexed with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Application of Structure-Based Design and Parallel Chemistry to Identify a Potent, Selective, and Brain Penetrant Phosphodiesterase 2A Inhibitor.

Helal, C.J.Arnold, E.P.Boyden, T.L.Chang, C.Chappie, T.A.Fennell, K.F.Forman, M.D.Hajos, M.Harms, J.F.Hoffman, W.E.Humphrey, J.M.Kang, Z.Kleiman, R.J.Kormos, B.L.Lee, C.W.Lu, J.Maklad, N.McDowell, L.Mente, S.O'Connor, R.E.Pandit, J.Piotrowski, M.Schmidt, A.W.Schmidt, C.J.Ueno, H.Verhoest, P.R.Yang, E.X.

(2017) J. Med. Chem. 60: 5673-5698

  • DOI: 10.1021/acs.jmedchem.7b00397
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphodiesterase 2A (PDE2A) inhibitors have been reported to demonstrate in vivo activity in preclinical models of cognition. To more fully explore the biology of PDE2A inhibition, we sought to identify potent PDE2A inhibitors with improved brain pe ...

    Phosphodiesterase 2A (PDE2A) inhibitors have been reported to demonstrate in vivo activity in preclinical models of cognition. To more fully explore the biology of PDE2A inhibition, we sought to identify potent PDE2A inhibitors with improved brain penetration as compared to current literature compounds. Applying estimated human dose calculations while simultaneously leveraging synthetically enabled chemistry and structure-based drug design has resulted in a highly potent, selective, brain penetrant compound 71 (PF-05085727) that effects in vivo biochemical changes commensurate with PDE2A inhibition along with behavioral and electrophysiological reversal of the effects of NMDA antagonists in rodents. This data supports the ability of PDE2A inhibitors to potentiate NMDA signaling and their further development for clinical cognition indications.


    Organizational Affiliation

    Pfizer Worldwide Research and Development , Eastern Point Road, Groton, Connecticut 06340, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent 3',5'-cyclic phosphodiesterase
A, B, C
345Homo sapiensMutation(s): 0 
Gene Names: PDE2A
EC: 3.1.4.17
Find proteins for O00408 (Homo sapiens)
Go to Gene View: PDE2A
Go to UniProtKB:  O00408
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
7Y4
Query on 7Y4

Download SDF File 
Download CCD File 
A, B, C
(3R)-1-{3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl}-N,N-dimethylpyrrolidin-3-amine
C24 H30 N8
CRNMQZGODAGJNN-GOSISDBHSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 168.021α = 90.00
b = 73.922β = 109.51
c = 92.136γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection
REFMACphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-12-12 
  • Released Date: 2017-06-28 
  • Deposition Author(s): Pandit, J., Parris, K.

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-07-26
    Type: Database references