4AEL

PDE10A in complex with the inhibitor AZ5

• PDB DOI: https://doi.org/10.2210/pdb4AEL/pdb

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


• Deposited: 2012-01-11 Released: 2012-01-25 
• Deposition Author(s): Bauer, U., Giordanetto, F., Bauer, M., OMahony, G., Johansson, K.E., Knecht, W., Hartleib-Geschwindner, J., Toppner Carlsson, E., Enroth, C., Sjogren, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Discovery of 4-Hydroxy-1,6-Naphthyridine-3-Carbonitrile Derivatives as Novel Pde10A Inhibitors.

Bauer, U., Giordanetto, F., Bauer, M., O'Mahony, G., Johansson, K.E., Knecht, W., Hartleib-Geschwindner, J., Carlsson, E.T., Enroth, C.

(2012) Bioorg Med Chem Lett 22: 1944

• PubMed: 22321214 
• DOI: https://doi.org/10.1016/j.bmcl.2012.01.046
• Primary Citation of Related Structures:  
  4AEL


• PubMed Abstract: 
  

  A series of 1,6-naphthyridine-based compounds was synthesized as potent phosphodiesterase 10A (PDE10A) inhibitors. Structure-based chemical modifications of the discovered chemotype served to further improve potency and selectivity over DHODH, laying the foundation for future optimization efforts.

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Organizational Affiliation: 

AstraZeneca, R&D Mölndal, Pepparedsleden 1, S-431 83 Mölndal, Sweden. [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: 79.84 kDa 
• Atom Count: 5,579 
• Modelled Residue Count: 643 
• Deposited Residue Count: 688 
• 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	344	Homo sapiens	Mutation(s): 0  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
4HN	E [auth A], H [auth B]	2-(2'-ETHOXYBIPHENYL-4-YL)-4-HYDROXY-1,6-NAPHTHYRIDINE-3-CARBONITRILE C23 H17 N3 O2 IMYDUDGJIZQSHN-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

Binding Affinity Annotations
ID	Source	Binding Affinity
4HN	PDBBind:  4AEL	IC50: 12 (nM) from 1 assay(s)
	BindingDB:  4AEL	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.966	α = 90
b = 81.688	β = 90
c = 160.469	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Bauer, U., Giordanetto, F., Bauer, M., OMahony, G., Johansson, K.E., Knecht, W., Hartleib-Geschwindner, J., Toppner Carlsson, E., Enroth, C., Sjogren, T.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-08-15
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description