7BPI

The crystal structue of PDE10A complexed with 14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of highly selective and orally available benzimidazole-based phosphodiesterase 10 inhibitors with improved solubility and pharmacokinetic properties for treatment of pulmonary arterial hypertension.

Yang, Y.Zhang, S.Zhou, Q.Zhang, C.Gao, Y.Wang, H.Li, Z.Wu, D.Wu, Y.Huang, Y.Y.Guo, L.Luo, H.B.

(2020) Acta Pharm Sin B 10: 2339-2347

  • DOI: https://doi.org/10.1016/j.apsb.2020.04.003
  • Primary Citation of Related Structures:  
    7BPI

  • PubMed Abstract: 

    Optimization efforts were devoted to discover novel PDE10A inhibitors in order to improve solubility and pharmacokinetics properties for a long-term therapy against pulmonary arterial hypertension (PAH) starting from the previously synthesized inhibitor A . As a result, a potent and highly selective PDE10A inhibitor, 14· 3HCl (half maximal inhibitory concentration, IC 50  = 2.8 nmol/L and > 3500-fold selectivity) exhibiting desirable solubility and metabolic stability with a remarkable bioavailability of 50% was identified with the aid of efficient methods of binding free energy predictions. Animal PAH studies showed that the improvement offered by 14· 3HCl [2.5 mg/kg, oral administration ( p.o .)] was comparable to tadalafil (5.0 mg/kg, p.o .), verifying the feasibility of PDE10A inhibitors for the anti-PAH treatment. The crystal structure of the PDE10A- 14 complex illustrates their binding pattern, which provided a guideline for rational design of highly selective PDE10A inhibitors.


  • 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 (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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.941α = 90
b = 81.683β = 90
c = 162.493γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
CrysalisProdata scaling
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)China21572279
National Natural Science Foundation of China (NSFC)China21708052
National Natural Science Foundation of China (NSFC)China21877134
National Natural Science Foundation of China (NSFC)China81602955
National Natural Science Foundation of China (NSFC)China81703341

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description