3WS8

Crystal structure of PDE10A in complex with a benzimidazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3WS8/pdb

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


• Deposited: 2014-03-04 Released: 2014-06-04 
• Deposition Author(s): Amano, Y., Honbou, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.314 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 

Starting Model: experimental

Literature

Novel benzimidazole derivatives as phosphodiesterase 10A (PDE10A) inhibitors with improved metabolic stability.

Chino, A., Masuda, N., Amano, Y., Honbou, K., Mihara, T., Yamazaki, M., Tomishima, M.

(2014) Bioorg Med Chem 22: 3515-3526

• PubMed: 24837154 
• DOI: https://doi.org/10.1016/j.bmc.2014.04.023
• Primary Citation of Related Structures:  
  3WS8, 3WS9


• PubMed Abstract: 
  

  In this study, we report the identification of potent benzimidazoles as PDE10A inhibitors. We first identified imidazopyridine 1 as a high-throughput screening hit compound from an in-house library. Next, optimization of the imidazopyridine moiety to improve inhibitory activity gave imidazopyridinone 10b. Following further structure-activity relationship development by reducing lipophilicity and introducing substituents, we acquired 35, which exhibited both improved metabolic stability and reduced CYP3A4 time-dependent inhibition.

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Organizational Affiliation: 

Institute for Drug Discovery Research, 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 and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.13 kDa 
• Atom Count: 5,337 
• 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
X4C	E [auth A], H [auth B]	8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine C23 H21 N5 VOYXDWSUNQJWTO-UHFFFAOYSA-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
X4C	BindingDB:  3WS8	IC50: 210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.314 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.31	α = 90
b = 81.107	β = 90
c = 160.47	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Amano, Y., Honbou, K.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description