8DI4

Discovery of MK-8189, a highly potent and selective PDE10A inhibitor for the treatment of schizophrenia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of MK-8189, a Highly Potent and Selective PDE10A Inhibitor for the Treatment of Schizophrenia.

Layton, M.E.Kern, J.C.Hartingh, T.J.Shipe, W.D.Raheem, I.Kandebo, M.Hayes, R.P.Huszar, S.Eddins, D.Ma, B.Fuerst, J.Wollenberg, G.K.Li, J.Fritzen, J.McGaughey, G.B.Uslaner, J.M.Smith, S.M.Coleman, P.J.Cox, C.D.

(2023) J Med Chem 66: 1157-1171

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01521
  • Primary Citation of Related Structures:  
    8DI4

  • PubMed Abstract: 

    PDE10A is an important regulator of striatal signaling that, when inhibited, can normalize dysfunctional activity. Given the involvement of dysfunctional striatal activity with schizophrenia, PDE10A inhibition represents a potentially novel means for its treatment. With the goal of developing PDE10A inhibitors, early optimization of a fragment hit through rational design led to a series of potent pyrimidine PDE10A inhibitors that required further improvements in physicochemical properties, off-target activities, and pharmacokinetics. Herein we describe the discovery of an isomeric pyrimidine series that addresses the liabilities seen with earlier compounds and resulted in the invention of compound 18 (MK-8189), which is currently in Phase 2b clinical development for the treatment of schizophrenia.


  • Organizational Affiliation

    Discovery Chemistry, Merck & Co., Inc., West Point, Pennsylvania 19486, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
A, B
345Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y233
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S9I (Subject of Investigation/LOI)
Query on S9I

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
2-methyl-6-{[(1S,2S)-2-(5-methylpyridin-2-yl)cyclopropyl]methoxy}-N-[(5-methyl-1,3,4-thiadiazol-2-yl)methyl]pyrimidin-4-amine
C19 H22 N6 O S
WQKPZDLZRFTMTI-CABCVRRESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.73α = 90
b = 81.36β = 90
c = 157.749γ = 90
Software Package:
Software NamePurpose
autoPROCdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoBUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description