2O8H | pdb_00002o8h

Crystal structure of the catalytic domain of rat phosphodiesterase 10A

• PDB DOI: https://doi.org/10.2210/pdb2O8H/pdb

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


• Deposited: 2006-12-12 Released: 2007-01-09 
• Deposition Author(s): Pandit, J., Marr, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: in silico

Literature

Discovery of a series of 6,7-dimethoxy-4-pyrrolidylquinazoline PDE10A inhibitors

Chappie, T.A., Humphrey, J.M., Allen, M.P., Estep, K.G., Fox, C.B., Lebel, L.A., Liras, S., Marr, E.S., Menniti, F.S., Pandit, J., Schmidt, C.J., Tu, M., Williams, R.D., Yang, F.V.

(2007) J Med Chem 50: 182-185

• PubMed: 17228859 
• DOI: https://doi.org/10.1021/jm060653b
• Primary Citation Related Structures: 
  2O8H, 2OVV, 2OVY


• PubMed Abstract: 
  

  A papaverine based pharmacophore model for PDE10A inhibition was generated via SBDD and used to design a library of 4-amino-6,7-dimethoxyquinazolines. From this library emerged an aryl ether pyrrolidyl 6,7-dimethoxyquinazoline series that became the focal point for additional modeling, X-ray, and synthetic efforts toward increasing PDE10A inhibitory potency and selectivity versus PDE3A/B. These efforts culminated in the discovery of 29, a potent and selective brain penetrable inhibitor of PDE10A.

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Organizational Affiliation: 
• CNS Discovery and Experimental Medicinal Sciences, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 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: 42.24 kDa 
• Atom Count: 2,839 
• Modeled Residue Count: 307 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphodiesterase-10A	A	362	Rattus norvegicus	Mutation(s): 0  Gene Names: Pde10a, PDE10A EC: 3.1.4.17
UniProt
Find proteins for Q9QYJ6 (Rattus norvegicus) Explore Q9QYJ6  Go to UniProtKB:  Q9QYJ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
227	D [auth A]	6,7-DIMETHOXY-4-{8-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]-3,4-DIHYDROISOQUINOLIN-2(1H)-YL}QUINAZOLINE C24 H29 N5 O4 S XOFGGFSZAJCEEW-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
227	BindingDB:  2O8H	Ki: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.273 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.622	α = 90
b = 120.622	β = 90
c = 82.143	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-09 
Deposition Author(s): Pandit, J., Marr, E.S.

Revision History  

• Version 1.0: 2007-01-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description