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


Ligand Structure Quality Assessment 


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, 3JSW

  • 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9AA, B329Homo sapiensMutation(s): 0 
Gene Names: PDE9A
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76083 (Homo sapiens)
Explore O76083 
Go to UniProtKB:  O76083
PHAROS:  O76083
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76083
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WTC
Query on WTC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth 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 Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
WTC PDBBind:  3JSI IC50: 2.1 (nM) from 1 assay(s)
BindingDB:  3JSI IC50: min: 0.8, max: 2.1 (nM) from 2 assay(s)
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



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • 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