3JSW

Human PDE9 in complex with selective inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 

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:  3JSI

  • 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 sapiensGene 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

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

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Download CCD File 
A, B
6-[(3S,4S)-1-benzyl-4-methylpyrrolidin-3-yl]-1-(1-methylethyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C20 H25 N5 O
PUGMRQMXTZPAIZ-RHSMWYFYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JARIC50: 66 nM (100) BINDINGDB
JARIC50: 66 nM BINDINGMOAD
JARIC50: 66 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.278α = 90.00
b = 103.278β = 90.00
c = 270.349γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-09-11 
  • 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: Advisory, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description