4QGE | pdb_00004qge

phosphodiesterase-9A in complex with inhibitor WYQ-C36D

• PDB DOI: https://doi.org/10.2210/pdb4QGE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Pan troglodytes
• Mutation(s): No 


• Deposited: 2014-05-22 Released: 2014-12-10 
• Deposition Author(s): Shao, Y.-X., Huang, M., Cui, W., Ke, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.241 (DCC) 

Starting Model: experimental

Literature

Discovery of a Phosphodiesterase 9A Inhibitor as a Potential Hypoglycemic Agent.

Shao, Y.X., Huang, M., Cui, W., Feng, L.J., Wu, Y., Cai, Y., Li, Z., Zhu, X., Liu, P., Wan, Y., Ke, H., Luo, H.B.

(2014) J Med Chem 57: 10304-10313

• PubMed: 25432025 
• DOI: https://doi.org/10.1021/jm500836h
• Primary Citation Related Structures: 
  4QGE


• PubMed Abstract: 
  

  Phosphodiesterase 9 (PDE9) inhibitors have been studied as potential therapeutics for treatment of diabetes and Alzheimer's disease. Here we report a potent PDE9 inhibitor 3r that has an IC50 of 0.6 nM and >150-fold selectivity over other PDEs. The HepG2 cell-based assay shows that 3r inhibits the mRNA expression of phosphoenolpyruvate carboxykinase and glucose 6-phosphatase. These activities of 3r, together with the reasonable pharmacokinetic properties and no acute toxicity at 1200 mg/kg dosage, suggest its potential as a hypoglycemic agent. The crystal structure of PDE9-3r reveals significantly different conformation and hydrogen bonding pattern of 3r from those of previously published 28s. Both 3r and 28s form a hydrogen bond with Tyr424, a unique PDE9 residue (except for PDE8), but 3r shows an additional hydrogen bond with Ala452. This structure information might be useful for design of PDE9 inhibitors.

---

Organizational Affiliation: 
• School of Pharmaceutical Sciences, Sun Yat-Sen University , Guangzhou 510006, P. R. China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.55 kDa 
• Atom Count: 5,665 
• Modeled Residue Count: 642 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase 9A	A, B	533	Pan troglodytes	Mutation(s): 0  Gene Names: PDE9A EC: 3.1.4.35
UniProt
Find proteins for H2QL32 (Pan troglodytes) Explore H2QL32  Go to UniProtKB:  H2QL32

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
35O	C [auth A], F [auth B]	N~2~-(1-cyclopentyl-4-oxo-4,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl)-N-(4-methoxyphenyl)-D-alaninamide C20 H24 N6 O3 UBBCZBKJYNXHGT-GFCCVEGCSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.241 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.58	α = 90
b = 103.58	β = 90
c = 268.657	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Shao, Y.-X., Huang, M., Cui, W., Ke, H.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary