6K9U | pdb_00006k9u

Discovery of Pyrazolo[1,5-a]pyrimidine Derivative as a Highly Selective PDE10A Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.215 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Discovery of a pyrazolo[1,5-a]pyrimidine derivative (MT-3014) as a highly selective PDE10A inhibitor via core structure transformation from the stilbene moiety.

Koizumi, Y., Tanaka, Y., Matsumura, T., Kadoh, Y., Miyoshi, H., Hongu, M., Takedomi, K., Kotera, J., Sasaki, T., Taniguchi, H., Watanabe, Y., Takakuwa, M., Kojima, K., Baba, N., Nakamura, I., Kawanishi, E.

(2019) Bioorg Med Chem 27: 3440-3450

  • DOI: https://doi.org/10.1016/j.bmc.2019.06.021
  • Primary Citation Related Structures: 
    6K9U

  • PubMed Abstract: 

    We have developed a new class of PDE10A inhibitor, a pyrazolo[1,5-a]pyrimidine derivative MT-3014 (1). A previous compound introduced was deprioritized due to concerns for E/Z-isomerization and glutathione-adduct formation at the core stilbene structure. We discovered pyrazolo [1,5-a] pyrimidine as a new lead scaffold by structure-based drug design utilizing a co-crystal structure with PDE10A. The lead compound was optimized for in vitro activity, solubility, and selectivity against human ether-á-go-go related gene cardiac channel binding. We observed that MT-3014 shows excellent efficacy in rat conditioned avoidance response test and suitable pharmacokinetic properties in rats, especially high brain penetration.

    • Organizational Affiliation: 
    • Sohyaku. Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama 227-0033, Japan. Electronic address: koizumi.yuuki@me.mt-pharma.co.jp.

Macromolecule Content 

  • Total Structure Weight: 36.54 kDa 
  • Atom Count: 2,630 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 311 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A311Rattus norvegicusMutation(s): 0 
Gene Names: Pde10a
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt
Find proteins for Q9QYJ6 (Rattus norvegicus)
Explore Q9QYJ6 
Go to UniProtKB:  Q9QYJ6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QYJ6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.215 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.456α = 90
b = 120.456β = 90
c = 83.899γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Advisory, Data collection, Database references, Derived calculations