5C2H | pdb_00005c2h

PDE10 complexed with 6-chloro-N-[(2,4-dimethylthiazol-5-yl)methyl]-5-methyl-2-[3-(2-quinolyl)propoxy]pyrimidin-4-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.240 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 83.97 kDa 
  • Atom Count: 5,173 
  • Modeled Residue Count: 630 
  • Deposited Residue Count: 724 
  • 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
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

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4XU

Query on 4XU



Download:Ideal Coordinates CCD File
H [auth B]6-chloro-N-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]-5-methyl-2-[3-(quinolin-2-yl)propoxy]pyrimidin-4-amine
C23 H24 Cl N5 O S
DWLPNEAIQATTGD-UHFFFAOYSA-N
4PX

Query on 4PX



Download:Ideal Coordinates CCD File
E [auth A]3-(1-hydroxy-2-methylpropan-2-yl)-5-phenyl-3,5-dihydro-1H-imidazo[4,5-c][1,8]naphthyridine-2,4-dione
C19 H18 N4 O3
ZQRNBXXBVMUYDO-UHFFFAOYSA-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
4XU BindingDB:  5C2H Ki: min: 8.00e-3, max: 8.20e-3 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.240 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.657α = 90
b = 81.28β = 90
c = 157.101γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-10-07 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.4: 2024-11-20
    Changes: Structure summary