5TZA

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A WITH 3-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl-1-[(naphthalene-2-yl)carbonyl]piperidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.

Gomez, L.Massari, M.E.Vickers, T.Freestone, G.Vernier, W.Ly, K.Xu, R.McCarrick, M.Marrone, T.Metz, M.Yan, Y.G.Yoder, Z.W.Lemus, R.Broadbent, N.J.Barido, R.Warren, N.Schmelzer, K.Neul, D.Lee, D.Andersen, C.B.Sebring, K.Aertgeerts, K.Zhou, X.Tabatabaei, A.Peters, M.Breitenbucher, J.G.

(2017) J. Med. Chem. 60: 2037-2051

  • DOI: 10.1021/acs.jmedchem.6b01793
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of potent and selective [1,2,4]triazolo[1,5-a]pyrimidine PDE2a inhibitors is reported. The design and improvement of the binding properties of this series was achieved using X-ray crystal structures in conjunction with careful analysis of el ...

    A series of potent and selective [1,2,4]triazolo[1,5-a]pyrimidine PDE2a inhibitors is reported. The design and improvement of the binding properties of this series was achieved using X-ray crystal structures in conjunction with careful analysis of electronic and structural requirements for the PDE2a enzyme. One of the lead compounds, compound 27 (DNS-8254), was identified as a potent and highly selective PDE2a enzyme inhibitor with favorable rat pharmacokinetic properties. Interestingly, the increased potency of compound 27 was facilitated by the formation of a halogen bond with the oxygen of Tyr827 present in the PDE2a active site. In vivo, compound 27 demonstrated significant memory enhancing effects in a rat model of novel object recognition. Taken together, these data suggest that compound 27 may be a useful tool to explore the pharmacology of selective PDE2a inhibition.


    Organizational Affiliation

    Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent 3',5'-cyclic phosphodiesterase
A, B, C, D
344Homo 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, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
7OG
Query on 7OG

Download SDF File 
Download CCD File 
A, B, C, D
[(3S)-3-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](naphthalen-2-yl)methanone
C22 H21 N5 O
TXIOKRWXRUIBEA-IBGZPJMESA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.799α = 109.36
b = 73.444β = 91.17
c = 91.614γ = 91.14
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-11-21 
  • Released Date: 2017-02-22 
  • Deposition Author(s): Xu, R., Aertgeerts, K.

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-03-29
    Type: Data collection
  • Version 1.3: 2017-11-22
    Type: Refinement description