4P1R | pdb_00004p1r

Crystal Structure of PDE10A with Imidazo[4,5-b]pyridines as Potent and Selective Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.189 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.153 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4P1R

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of Novel Imidazo[4,5-b]pyridines as Potent and Selective Inhibitors of Phosphodiesterase 10A (PDE10A).

Hu, E.Andrews, K.Chmait, S.Zhao, X.Davis, C.Miller, S.Hill Della Puppa, G.Dovlatyan, M.Chen, H.Lester-Zeiner, D.Able, J.Biorn, C.Ma, J.Shi, J.Treanor, J.Allen, J.R.

(2014) ACS Med Chem Lett 5: 700-705

  • DOI: https://doi.org/10.1021/ml5000993
  • Primary Citation Related Structures: 
    4P0N, 4P1R

  • PubMed Abstract: 

    We report the discovery of novel imidazo[4,5-b]pyridines as potent and selective inhibitors of PDE10A. The investigation began with our recently disclosed ketobenzimidazole 1, which exhibited single digit nanomolar PDE10A activity but poor oral bioavailability. To improve oral bioavailability, we turned to novel scaffold imidazo[4,5-b]pyridine 2, which not only retained nanomolar PDE10A activity but was also devoid of the morpholine metabolic liability. Structure-activity relationship studies were conducted systematically to examine how various regions of the molecule impacted potency. X-ray cocrystal structures of compounds 7 and 24 in human PDE10A helped to elucidate the key bonding interactions. Five of the most potent and structurally diverse imidazo[4,5-b]pyridines (4, 7, 12b, 24a, and 24b) with PDE10A IC50 values ranging from 0.8 to 6.7 nM were advanced into receptor occupancy studies. Four of them (4, 12b, 24a, and 24b) achieved 55-74% RO at 10 mg/kg po.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Department of Molecular Structure, Department of Pharmacokinetics and Drug Metabolism, and Department of Neuroscience, Amgen, Inc. , One Amgen Center Drive, Thousand Oaks, California 93012-1799, United States.

Macromolecule Content 

  • Total Structure Weight: 81.94 kDa 
  • Atom Count: 6,007 
  • Modeled Residue Count: 626 
  • Deposited Residue Count: 676 
  • 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
338Homo 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
2KR

Query on 2KR



Download:Ideal Coordinates CCD File
PA [auth B],
V [auth A]
N-[4-(2-methoxy-3H-imidazo[4,5-b]pyridin-3-yl)phenyl]-5-methylpyridin-2-amine
C19 H17 N5 O
ZAIBUTICQXDSIC-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
N [auth A],
O [auth A],
U [auth A],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
MA [auth B]
NA [auth B]
OA [auth B]
P [auth A]
Q [auth A]
MA [auth B],
NA [auth B],
OA [auth B],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
W [auth B],
X [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.189 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 252.971α = 90
b = 252.971β = 90
c = 252.971γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-07-23 
  • Deposition Author(s): Chmait, S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy