3JSI

Human phosphodiesterase 9 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification of a Brain Penetrant PDE9A Inhibitor Utilizing Prospective Design and Chemical Enablement as a Rapid Lead Optimization Strategy.

Verhoest, P.R.Proulx-Lafrance, C.Corman, M.Chenard, L.Helal, C.J.Hou, X.Kleiman, R.Liu, S.Marr, E.Menniti, F.S.Schmidt, C.J.Vanase-Frawley, M.Schmidt, A.W.Williams, R.D.Nelson, F.R.Fonseca, K.R.Liras, S.

(2009) J.Med.Chem. 52: 7946-7949

  • DOI: 10.1021/jm9015334
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • By use of chemical enablement and prospective design, a novel series of selective, brain penetrant PDE9A inhibitors have been identified that are capable of producing in vivo elevations of brain cGMP.

    By use of chemical enablement and prospective design, a novel series of selective, brain penetrant PDE9A inhibitors have been identified that are capable of producing in vivo elevations of brain cGMP.


    Organizational Affiliation

    Neuroscience Chemistry, Pfizer Global Research and Development, Groton, CT 06340, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
A, B
329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
Find proteins for O76083 (Homo sapiens)
Go to Gene View: PDE9A
Go to UniProtKB:  O76083
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
WTC
Query on WTC

Download SDF File 
Download CCD File 
A, B
6-benzyl-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C17 H18 N4 O
FVOYQCUKGQGDKH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WTCIC50: 0.8 - 2.1 nM (100) BINDINGDB
WTCIC50: 2.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.099α = 90.00
b = 104.099β = 90.00
c = 271.040γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
BUSTERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-10 
  • Released Date: 2009-12-01 
  • Deposition Author(s): Liu, S.

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description