5C29 | pdb_00005c29

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4XYClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

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.


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
362Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.234 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.48α = 90
b = 81.19β = 90
c = 152.99γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 4XYClick on this verticalbar to view details

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
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary