4DDL

PDE10a Crystal Structure Complexed with Novel Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report



Literature

Discovery of potent, selective, and metabolically stable 4-(pyridin-3-yl)cinnolines as novel phosphodiesterase 10A (PDE10A) inhibitors.

Hu, E., Kunz, R.K., Rumfelt, S., Chen, N., Burli, R., Li, C., Andrews, K.L., Zhang, J., Chmait, S., Kogan, J., Lindstrom, M., Hitchcock, S.A., Treanor, J.

(2012) Bioorg Med Chem Lett 22: 2262-2265

  • DOI: 10.1016/j.bmcl.2012.01.086
  • Primary Citation of Related Structures:  
    4DDL

  • PubMed Abstract: 

    • We report the discovery of 6,7-dimethoxy-4-(pyridin-3-yl)cinnolines as novel inhibitors of phosphodiesterase 10A (PDE10A). Systematic examination and analyses of structure-activity-relationships resulted in single digit nM potency against PDE10A. X-ray c ...

    We report the discovery of 6,7-dimethoxy-4-(pyridin-3-yl)cinnolines as novel inhibitors of phosphodiesterase 10A (PDE10A). Systematic examination and analyses of structure-activity-relationships resulted in single digit nM potency against PDE10A. X-ray co-crystal structure revealed the mode of binding in the enzyme's catalytic domain and the source of selectivity against other PDEs. High in vivo clearance in rats was addressed with the help of metabolite identification (ID) studies. These findings combined resulted in compound 39, a promising potent inhibitor of PDE10A with good in vivo metabolic stability in rats and efficacy in a rodent behavioral model.

    Organizational Affiliation: 

    Department of Small Molecule Chemistry, Amgen Inc., Thousand Oaks, CA 91320-1799, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A A, B338Homo sapiensMutation(s): 0 
Gene Names: PDE10A
EC: 3.1.4.17 (PDB Primary Data), 3.1.4.35 (PDB Primary Data)
Find proteins for Q9Y233 (Homo sapiens)
Explore Q9Y233 
Go to UniProtKB:  Q9Y233
NIH Common Fund Data Resources
PHAROS:  Q9Y233
GTEx:  ENSG00000112541
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0JQ
Query on 0JQ
Download Ideal Coordinates CCD File 
A, B
2-{1-[5-(6,7-dimethoxycinnolin-4-yl)-3-methylpyridin-2-yl]piperidin-4-yl}propan-2-ol
C24 H30 N4 O3
PPAWFHDEPAUENY-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0JQIC50:  4.900000095367432   nM  BindingDB
0JQIC50:  4.900000095367432   nM  Binding MOAD
0JQIC50 :  4.900000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 252.964α = 90
b = 252.964β = 90
c = 252.964γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release