9JA8 | pdb_00009ja8

Crystal structure of human phosphodiesterase 10A in complex with N-(2-amino-2-thioxoethyl)-2-(3-(3-(dimethylcarbamoyl)-6-fluoroimidazo[1,2-a]pyridin-2-yl)azetidin-1-yl)quinoline-4-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.229 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9JA8

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Inhalable Carbonyl Sulfide Donor-Hybridized Selective Phosphodiesterase 10A Inhibitor for Treating Idiopathic Pulmonary Fibrosis by Inhibiting Tumor Growth Factor-beta Signaling and Activating the cAMP/Protein Kinase A/cAMP Response Element-Binding Protein (CREB)/p53 Axis.

Wang, Q.Liu, X.Yuan, H.Zhang, F.Wu, J.Yang, D.Qian, J.Huang, Y.Y.Chai, G.Luo, H.B.Guo, L.

(2025) Acs Pharmacol Transl Sci 8: 256-269

  • DOI: https://doi.org/10.1021/acsptsci.4c00671
  • Primary Citation Related Structures: 
    9JA8

  • PubMed Abstract: 

    Idiopathic pulmonary fibrosis (IPF) is a debilitating, incurable, and life-threatening disease that lacks effective therapy. The overexpression of phosphodiesterase 10A (PDE10A) plays a vital role in pulmonary fibrosis (PF). However, the impact of selective PDE10A inhibitors on the tumor growth factor-β (TGF-β)/small mother against decapentaplegic (Smad) signaling pathway remains unclear. Herein, we have exploited a novel carbonyl sulfide (COS)/hydrogen sulfide (H 2 S)-donor hybrid PDE10A inhibitor called COS-2080 with a well-defined mechanism of H 2 S-releasing action. It exhibited highly potent inhibitory activity against PDE10A and excellent PDE subfamily selectivity. Moreover, COS-2080 demonstrated significant antifibrotic effects by inhibiting cell proliferation and mitigating fibroblast-to-myofibroblast transition (FMT). A dry powder inhalation formulation called COS-2080-DPI has been developed using the ultrasonic spray freeze drying (USFD) technique, demonstrating significant antifibrotic efficacy in mice with bleomycin-induced PF at a dosage approximately 600 times lower than pirfenidone. This remarkable antifibrotic efficacy of COS-2080 on TGF-β1-induced FMT could be primarily attributed to its inhibition of the Smad2/Smad3 phosphorylation. Moreover, COS-2080 effectively attenuated fibrosis in MRC-5 cells by activating the cAMP/protein kinase A (PKA)/CREB pathway and potentially increasing levels of p53 protein. Our findings suggest that effective inhibition of PDE10A potentially confers a protective effect on FMT in PF by impeding TGF-β signaling and activating the cAMP/PKA/CREB/p53 axis.


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

Macromolecule Content 

  • Total Structure Weight: 75.77 kDa 
  • Atom Count: 5,286 
  • Modeled Residue Count: 631 
  • Deposited Residue Count: 644 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
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
A1L31
(Subject of Investigation/LOI)

Query on A1L31



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
~{N}-(2-azanyl-2-sulfanylidene-ethyl)-2-[3-[3-(dimethylcarbamoyl)-6-fluoranyl-imidazo[1,2-a]pyridin-2-yl]azetidin-1-yl]quinoline-4-carboxamide
C25 H24 F N7 O2 S
ZCOFOZHMMNQONH-UHFFFAOYSA-N
ZN

Query on ZN



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

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.229 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.1α = 90
b = 81.43β = 90
c = 160.376γ = 90
Software Package:
Software NamePurpose
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)China22277154
National Natural Science Foundation of China (NSFC)China82003576

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release