6MSA | pdb_00006msa

Novel, potent, selective and brain penetrant phosphodiesterase 10A inhibitors

• PDB DOI: https://doi.org/10.2210/pdb6MSA/pdb

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


• Deposited: 2018-10-16 Released: 2019-01-09 
• Deposition Author(s): Jakob, C.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Novel, potent, selective, and brain penetrant phosphodiesterase 10A inhibitors.

Geneste, H., Drescher, K., Jakob, C., Laplanche, L., Ochse, M., Torrent, M.

(2019) Bioorg Med Chem Lett 29: 406-412

• PubMed: 30587449 
• DOI: https://doi.org/10.1016/j.bmcl.2018.12.029
• Primary Citation Related Structures: 
  6MSA, 6MSC


• PubMed Abstract: 
  

  Herein we report the discovery of a novel series of phosphodiesterase 10A inhibitors. Optimization of a HTS hit (17) resulted in potent, selective, and brain penetrant 23 and 26; both exhibited much lower clearance in vivo and decreased volume of distribution (rat PK) and have thus the potential to inhibit the PDE10A target in vivo at a lower efficacious dose than the reference compound WEB-3.

---

Organizational Affiliation: 
• AbbVie Deutschland GmbH & Co. KG, Neuroscience Research, D-67008 Ludwigshafen, Germany. Electronic address: [e-mail].
AbbVie Deutschland GmbH & Co. KG, Neuroscience Research, D-67008 Ludwigshafen, Germany.
AbbVie, Structural Biology, IL 60064-6101, USA.
AbbVie Deutschland GmbH & Co. KG, DMPK, D-67008 Ludwigshafen, Germany.

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.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.15 kDa 
• Atom Count: 5,579 
• Modeled Residue Count: 651 
• Deposited Residue Count: 664 
• 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	332	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
JY4 (Subject of Investigation/LOI)	E [auth A]	7,8-dimethoxy-1-methyl-2H-pyrazolo[3,4-c]cinnoline C12 H12 N4 O2 NOAZBIGPIKIKDQ-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.54	α = 90
b = 82.2	β = 90
c = 158.4	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Jakob, C.G.

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations