3JSI | pdb_00003jsi

Human phosphodiesterase 9 in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3JSI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.218 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

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

• PubMed: 19919087 
• DOI: https://doi.org/10.1021/jm9015334
• Primary Citation 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.

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Organizational Affiliation: 
• Neuroscience Chemistry, Pfizer Global Research and Development, Groton, CT 06340, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.49 kDa 
• Atom Count: 5,489 
• Modeled Residue Count: 656 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A	A, B	329	Homo sapiens	Mutation(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 GTEx:  ENSG00000160191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WTC	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
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.218 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.099	α = 90
b = 104.099	β = 90
c = 271.04	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description