9JDU | pdb_00009jdu

The crystal structure of PDE10A complexed with inhibitor 2061


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.297 (Depositor), 0.305 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.248 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Discovery of novel azetidine-based imidazopyridines as selective and orally bioavailable inhibitors of phosphodiesterase 10A for the treatment of pulmonary arterial hypertension.

Huang, H.Xue, H.Cai, A.Yuan, H.Yao, Y.Liu, R.Yang, Y.Wang, Q.Li, Z.Liu, T.Huang, Y.Y.Dai, W.Luo, H.B.Zou, X.Wang, X.Guo, L.

(2025) Eur J Med Chem 290: 117537-117537

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117537
  • Primary Citation of Related Structures:  
    9JDU

  • PubMed Abstract: 

    Pulmonary arterial hypertension (PAH) is a chronic, progressive disorder of the pulmonary vasculature characterized by associated pulmonary and cardiac remodeling. Phosphodiesterase 10A (PDE10A) plays a crucial role in regulating cAMP concentration, thereby influencing pulmonary inflammation and pulmonary vascular remodeling. However, there is a lack of ideal PDE10A selective inhibitors available for PAH treatment. Herein, we employed structure-based drug design to develop a series of azetidine-based imidazopyridines, among which A30 demonstrated an IC 50 value of 3.5 nmol/L against PDE10A with high selectivity over other PDEs, low blood-brain barrier permeability, and improved drug-like properties. Oral administration of A30 exhibited significant anti-PAH effects not only in monocrotaline-induced rats, but also in Sugen/hypoxia(Su/Hx)-induced PH mice. Our findings indicate that A30 inhibits PDE10A to suppress pulmonary vascular remodeling through the activation of cAMP-associated signaling pathways.


  • Organizational Affiliation
    • School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
322Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
PHAROS:  Q9Y233
GTEx:  ENSG00000112541 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y233
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EBE (Subject of Investigation/LOI)
Query on A1EBE

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
ethyl 2-[1-[4-[2-(diethylaminomethylamino)ethanoyl]quinolin-2-yl]azetidin-3-yl]imidazo[1,2-a]pyridine-3-carboxylate
C29 H34 N6 O3
LHVNJVLZPILOCO-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.297 (Depositor), 0.305 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.248 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.509α = 90
b = 81.583β = 90
c = 159.744γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
CrysalisProdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82003576

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release