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 
  • R-Value Observed: 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:  
    3JSW, 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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9AAB329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
Find proteins for O76083 (Homo sapiens)
Explore O76083 
Go to UniProtKB:  O76083
NIH Common Fund Data Resources
PHAROS  O76083
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WTC
Query on WTC

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
ZN
Query on ZN

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

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WTCIC50 :  2.0999999046325684   nM  PDBBind
WTCIC50:  2.0999999046325684   nM  BindingDB
WTCIC50:  0.800000011920929   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.099α = 90
b = 104.099β = 90
c = 271.04γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description