6KDZ

Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Synthesis, SAR study, and biological evaluation of novel 2,3-dihydro-1H-imidazo[1,2-a]benzimidazole derivatives as phosphodiesterase 10A inhibitors.

Chino, A.Honda, S.Morita, M.Yonezawa, K.Hamaguchi, W.Amano, Y.Moriguchi, H.Yamazaki, M.Aota, M.Tomishima, M.Masuda, N.

(2019) Bioorg.Med.Chem. 27: 3692-3706

  • DOI: 10.1016/j.bmc.2019.07.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phosphodiesterase 10A (PDE10A) inhibitors were designed and synthesized based on the dihydro-imidazobenzimidazole scaffold. Compound 5a showed moderate inhibitory activity and good permeability, but unfavorable high P-glycoprotein (P-gp) liability fo ...

    Phosphodiesterase 10A (PDE10A) inhibitors were designed and synthesized based on the dihydro-imidazobenzimidazole scaffold. Compound 5a showed moderate inhibitory activity and good permeability, but unfavorable high P-glycoprotein (P-gp) liability for brain penetration. We performed an optimization study to improve both the P-gp efflux ratio and PDE10A inhibitory activity. As a result, 6d was identified with improved P-gp liability and high PDE10A inhibitory activity. Compound 6d also showed satisfactory brain penetration, suppressed phencyclidine-induced hyperlocomotion and improved MK-801-induced working memory deficit.


    Organizational Affiliation

    Functional Molecules, Modality Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan. Electronic address: ayaka.chino@astellas.com.,Functional Molecules, Modality Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
345Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17, 3.1.4.35
Find proteins for Q9Y233 (Homo sapiens)
Go to Gene View: PDE10A
Go to UniProtKB:  Q9Y233
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
D79
Query on D79

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Download CCD File 
A
4-[2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)ethyl]-3,7,8,10-tetrazatricyclo[7.4.0.0^{2,7}]trideca-1,3,5,8,10,12-hexaen-6-ol
C18 H16 N8 O
RWHNPVAUZAQFAE-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.253 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.218α = 90.00
b = 81.044β = 90.00
c = 162.136γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CrystalCleardata reduction
PDB_EXTRACTdata extraction
d*TREKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-07-03 
  • Released Date: 2019-08-14 
  • Deposition Author(s): Amano, Y., Honbou, K.

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release