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 9AA, B329Homo 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
GTEx  ENSG00000160191
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

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View more in-depth experimental data

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