5K9R | pdb_00005k9r

PDE10a with imidazopyrazine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5K9R/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-01 Released: 2016-08-24 
• Deposition Author(s): Gibbs, A.G., Schubert, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.322 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.236 (Depositor) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Discovery of novel potent imidazo[1,2-b]pyridazine PDE10a inhibitors.

Meegalla, S.K., Huang, H., Illig, C.R., Parks, D.J., Chen, J., Lee, Y.K., Wilson, K.J., Patel, S.K., Cheung, W.S., Lu, T., Kirchner, T., Askari, H.B., Geisler, J., Patch, R.J., Gibbs, A.C., Rady, B., Connelly, M., Player, M.R.

(2016) Bioorg Med Chem Lett 26: 4216-4222

• PubMed: 27491708 
• DOI: https://doi.org/10.1016/j.bmcl.2016.07.054
• Primary Citation Related Structures: 
  5K9R


• PubMed Abstract: 
  

  Design and optimization of a novel series of imidazo[1,2-b]pyridazine PDE10a inhibitors are described. Compound 31 displays excellent pharmacokinetic properties and was also evaluated as an insulin secretagogue in vitro and in vivo.

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Organizational Affiliation: 
• Janssen Research & Development, Welsh and McKean Roads, Spring House, PA 19477-0776, USA.
Janssen Research & Development, Welsh and McKean Roads, Spring House, PA 19477-0776, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.4 kDa 
• Atom Count: 5,157 
• Modeled Residue Count: 624 
• Deposited Residue Count: 624 
• 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, B	312	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6RC	E [auth A], H [auth B]	4-[5-[1-(2-methoxyethyl)pyrazol-4-yl]-2-(quinolin-2-yloxymethyl)imidazo[1,2-a]pyrazin-8-yl]morpholine C26 H27 N7 O3 FTYUTNBYQHNWNV-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.322 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.236 (Depositor) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.46	α = 90
b = 81.2	β = 90
c = 160.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-24 
Deposition Author(s): Gibbs, A.G., Schubert, C.

Revision History  

• Version 1.0: 2016-08-24
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary