6KE0

Crystal structure of PDE10A in complex with a triazolopyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6KE0/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.302 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 

Starting Model: experimental

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

• PubMed: 31301949 
• DOI: https://doi.org/10.1016/j.bmc.2019.07.010
• Primary Citation of Related Structures:  
  6KDX, 6KDZ, 6KE0


• 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 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.

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Organizational Affiliation: 

Functional Molecules, Modality Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.75 kDa 
• Atom Count: 5,289 
• Modelled Residue Count: 648 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A, B	345	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D7C (Subject of Investigation/LOI)	E [auth A]	2-(5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl)-1-[(2S)-2-methyl-1,2-dihydroimidazo[1,2-a]benzimidazol-3-yl]ethanone C19 H19 N7 O FWIWLYXORKTJJN-ZDUSSCGKSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D7C	BindingDB:  6KE0	IC50: min: 28, max: 69 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.302 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.398	α = 90
b = 81.553	β = 90
c = 160.763	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description