9WP3 | pdb_00009wp3

The crystal structure of PDE2A complexed with inhibitor 13j


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.311 (Depositor), 0.316 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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Literature

Discovery of novel 2,4,5,6-tetrahydro-7H-pyrazolo[3,4-c]pyridine-7-one derivatives as PDE2 inhibitors with Alzheimer's disease therapeutic potential.

Yang, F.Guo, Q.Chen, M.Wang, W.Chen, X.Zhang, S.Bian, H.Li, J.Jiao, Z.Wang, Q.Xiong, W.Huang, Y.Y.Liu, Y.Xu, C.Huang, L.

(2026) Eur J Med Chem 302: 118302-118302

  • DOI: https://doi.org/10.1016/j.ejmech.2025.118302
  • Primary Citation Related Structures: 
    9WP3

  • PubMed Abstract: 

    Phosphodiesterase 2 (PDE2), a dual-substrate cyclic nucleotide hydrolase, represents a potential therapeutic target for cognitive impairment. This study aims to develop 2,4,5,6-tetrahydro-7H-pyrazolo[3,4-c]pyridine-7-one-based PDE2 inhibitors with favorable drug-like properties for the treatment of Alzheimer's disease. Through scaffold hopping and cocrystal structure analysis, compound 14c was identified as an effective PDE2 inhibitor (IC 50  = 0.6 μM, aqueous solubility = 60.36 μg/mL). Moreover, 14c demonstrated favorable hepatic microsomal stability, pharmacokinetic properties (t 1/2  = 4.4 h, F% = 95.66 %) and promising safety both in vitro and in vivo. In the OKA-induced AD mice models, administration of 14c significantly improved memory deficits and cognitive impairment. Molecular mechanism studies revealed that the neuroprotective effects of 14c were mediated through the PKA/CREB/BDNF signaling pathway. Collectively, these findings represent significant advances in developing PDE2 inhibitors with favorable drug-like properties and establish a solid foundation for their therapeutic application in AD.


  • Organizational Affiliation
    • Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, China.

Macromolecule Content 

  • Total Structure Weight: 160.88 kDa 
  • Atom Count: 10,150 
  • Modeled Residue Count: 1,243 
  • Deposited Residue Count: 1,360 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cGMP-dependent 3',5'-cyclic phosphodiesterase
A, B, C, D
340Homo sapiensMutation(s): 0 
Gene Names: PDE2A
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O00408 (Homo sapiens)
Explore O00408 
Go to UniProtKB:  O00408
PHAROS:  O00408
GTEx:  ENSG00000186642 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00408
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1E46
(Subject of Investigation/LOI)

Query on A1E46



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
M [auth C],
P [auth D]
7-oxidanylidene-~{N}-[(1~{S})-1-[4-(trifluoromethyl)phenyl]propyl]-2,4,5,6-tetrahydropyrazolo[3,4-c]pyridine-3-carboxamide
C17 H17 F3 N4 O2
ABWGCLJAERQLEF-LBPRGKRZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C],
N [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.311 (Depositor), 0.316 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.264 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.782α = 109.62
b = 73.08β = 91.183
c = 91.114γ = 90.854
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22277019

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release