3HR1 | pdb_00003hr1

Discovery of novel inhibitors of PDE10A

• PDB DOI: https://doi.org/10.2210/pdb3HR1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-06-08 Released: 2009-08-04 
• Deposition Author(s): Pandit, J., Marr, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Discovery of a Novel Class of Phosphodiesterase 10A Inhibitors and Identification of Clinical Candidate 2-[4-(1-Methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)-phenoxymethyl]-quinoline (PF-2545920) for the Treatment of Schizophrenia

Verhoest, P.R., Chapin, D.S., Corman, M., Fonseca, K., Harms, J.F., Hou, X., Marr, E.S., Menniti, F.S., Nelson, F., O'Connor, R., Pandit, J., Proulx-Lafrance, C., Schmidt, A.W., Schmidt, C.J., Suiciak, J.A., Liras, S.

(2009) J Med Chem 52: 5188-5196

• PubMed: 19630403 
• DOI: https://doi.org/10.1021/jm900521k
• Primary Citation of Related Structures:  
  3HQW, 3HQY, 3HQZ, 3HR1


• PubMed Abstract: 
  

  By utilizing structure-based drug design (SBDD) knowledge, a novel class of phosphodiesterase (PDE) 10A inhibitors was identified. The structure-based drug design efforts identified a unique "selectivity pocket" for PDE10A inhibitors, and interactions within this pocket allowed the design of highly selective and potent PDE10A inhibitors. Further optimization of brain penetration and drug-like properties led to the discovery of 2-[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)-phenoxymethyl]-quinoline (PF-2545920). This PDE10A inhibitor is the first reported clinical entry for this mechanism in the treatment of schizophrenia.

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Organizational Affiliation: 

Neuroscience, Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.34 kDa 
• Atom Count: 2,986 
• Modelled Residue Count: 305 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A	A	380	Rattus norvegicus	Mutation(s): 0  Gene Names: Pde10a EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
UniProt
Find proteins for Q9QYJ6 (Rattus norvegicus) Explore Q9QYJ6  Go to UniProtKB:  Q9QYJ6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PF9	D [auth A]	2-{[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)phenoxy]methyl}quinoline C25 H20 N4 O AZEXWHKOMMASPA-UHFFFAOYSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PF9	BindingDB:  3HR1	Ki: 0.17 (nM) from 1 assay(s)
		IC50: min: 0.18, max: 0.65 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.66	α = 90
b = 120.66	β = 90
c = 83.21	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-04 
Deposition Author(s): Pandit, J., Marr, E.S.

Revision History  

• Version 1.0: 2009-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description