8DI4 | pdb_00008di4

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 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.252 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 80.16 kDa 
  • Atom Count: 5,314 
  • Modeled Residue Count: 642 
  • Deposited Residue Count: 690 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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
Binding Affinity Annotations 
IDSourceBinding Affinity
S9I BindingDB:  8DI4 Ki: 0.03 (nM) from 1 assay(s)
IC50: 1.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.295 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.252 (Depositor) 
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

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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
  • Version 1.2: 2024-11-20
    Changes: Structure summary