4E90

Human phosphodiesterase 9 in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report



Literature

Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors.

Claffey, M.M.Helal, C.J.Verhoest, P.R.Kang, Z.Fors, K.S.Jung, S.Zhong, J.Bundesmann, M.W.Hou, X.Lui, S.Kleiman, R.J.Vanase-Frawley, M.Schmidt, A.W.Menniti, F.Schmidt, C.J.Hoffman, W.E.Hajos, M.McDowell, L.O'Connor, R.E.Macdougall-Murphy, M.Fonseca, K.R.Becker, S.L.Nelson, F.R.Liras, S.

(2012) J Med Chem 55: 9055-9068

  • DOI: 10.1021/jm3009635
  • Primary Citation of Related Structures:  
    4G2J, 4G2L, 4E90

  • PubMed Abstract: 
  • Phosphodiesterase 9A inhibitors have shown activity in preclinical models of cognition with potential application as novel therapies for treating Alzheimer's disease. Our clinical candidate, PF-04447943 (2), demonstrated acceptable CNS permeability in rats with modest asymmetry between central and peripheral compartments (free brain/free plasma = 0 ...

    Phosphodiesterase 9A inhibitors have shown activity in preclinical models of cognition with potential application as novel therapies for treating Alzheimer's disease. Our clinical candidate, PF-04447943 (2), demonstrated acceptable CNS permeability in rats with modest asymmetry between central and peripheral compartments (free brain/free plasma = 0.32; CSF/free plasma = 0.19) yet had physicochemical properties outside the range associated with traditional CNS drugs. To address the potential risk of restricted CNS penetration with 2 in human clinical trials, we sought to identify a preclinical candidate with no asymmetry in rat brain penetration and that could advance into development. Merging the medicinal chemistry strategies of structure-based design with parallel chemistry, a novel series of PDE9A inhibitors was identified that showed improved selectivity over PDE1C. Optimization afforded preclinical candidate 19 that demonstrated free brain/free plasma ≥ 1 in rat and reduced microsomal clearance along with the ability to increase cyclic guanosine monophosphosphate levels in rat CSF.


    Organizational Affiliation

    Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. michelle.m.claffey@pfizer.com



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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7RG
Query on 7RG

Download CCD File 
A, B
6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin-3-yl]-1-(tetrahydro-2H-pyran-4-yl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
C20 H25 N7 O2
IWXUVYOOUMLUTQ-CZUORRHYSA-N
 Ligand Interaction
ZN
Query on ZN

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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 %)
7RGIC50:  8.300000190734863   nM  BindingDB
7RGIC50:  8   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.579α = 90
b = 103.579β = 90
c = 270.214γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-03-20 
  • Released Date: 2013-02-27 
  • Deposition Author(s): Liu, S.

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release