PDE10 complexed with 6-chloro-2-cyclopropyl-5-methyl-pyrimidin-4-amine

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 

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Discovery and Optimization of a Series of Pyrimidine-Based Phosphodiesterase 10A (PDE10A) Inhibitors through Fragment Screening, Structure-Based Design, and Parallel Synthesis.

Shipe, W.D.Sharik, S.S.Barrow, J.C.McGaughey, G.B.Theberge, C.R.Uslaner, J.M.Yan, Y.Renger, J.J.Smith, S.M.Coleman, P.J.Cox, C.D.

(2015) J Med Chem 58: 7888-7894

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b00983
  • Primary Citation of Related Structures:  
    5C1W, 5C28, 5C29, 5C2A, 5C2E, 5C2H

  • PubMed Abstract: 

    Screening of a fragment library for PDE10A inhibitors identified a low molecular weight pyrimidine hit with PDE10A Ki of 8700 nM and LE of 0.59. Initial optimization by catalog followed by iterative parallel synthesis guided by X-ray cocrystal structures resulted in rapid potency improvements with minimal loss of ligand efficiency. Compound 15 h, with PDE10A Ki of 8.2 pM, LE of 0.49, and >5000-fold selectivity over other PDEs, fully attenuates MK-801-induced hyperlocomotor activity after ip dosing.

  • Organizational Affiliation

    Departments of †Discovery Chemistry, ‡Chemistry Modeling and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories , West Point, Pennsylvania 19486, United States.

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
362Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y233
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
4XV BindingDB:  5C28 Ki: 2200 (nM) from 1 assay(s)
Binding MOAD:  5C28 Ki: 2200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.65α = 90
b = 82.04β = 90
c = 152.86γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2015-09-30 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references