4D09

PDE2a catalytic domain in complex with a brain penetrant inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4D09/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-04-24 Released: 2014-08-06 
• Deposition Author(s): Buijnsters, P., Andres, J.I., DeAngelis, M., Langlois, X., Rombouts, F., Sanderson, W., Tresadern, G., Trabanco, A., VanHoof, G., VanRoosbroeck, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 

Starting Model: other

Literature

Structure-Based Design of a Potent, Selective, and Brain Penetrating Pde2 Inhibitor with Demonstrated Target Engagement.

Buijnsters, P., De Angelis, M., Langlois, X., Rombouts, F.J.R., Sanderson, W., Tresadern, G., Ritchie, A., Trabanco, A.A., Vanhoof, G., Roosbroeck, Y.V., Andres, J.

(2014) ACS Med Chem Lett 5: 1049

• PubMed: 25221665 
• DOI: https://doi.org/10.1021/ml500262u
• Primary Citation of Related Structures:  
  4D08, 4D09


• PubMed Abstract: 
  

  Structure-guided design led to the identification of the novel, potent, and selective phosphodiesterase 2 (PDE2) inhibitor 12. Compound 12 demonstrated a >210-fold selectivity versus PDE10 and PDE11 and was inactive against all other PDE family members up to 10 μM. In vivo evaluation of 12 provided evidence that it is able to engage the target and to increase cGMP levels in relevant brain regions. Hence, 12 is a valuable tool compound for the better understanding of the role of PDE2 in cognitive impairment and other central nervous system related disorders.

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Organizational Affiliation: 

Neuroscience Medicinal Chemistry, Janssen Research & Development, a Division of Janssen Pharmaceutica NV , Turnhoutseweg 30, 2340 Beerse, Belgium.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 167.66 kDa 
• Atom Count: 11,118 
• Modelled Residue Count: 1,333 
• Deposited Residue Count: 1,412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CGMP-DEPENDENT 3', 5'-CYCLIC PHOSPHODIESTERASE	A, B, C, D	353	Homo sapiens	Mutation(s): 0  EC: 3.1.4.17
UniProt & NIH Common Fund Data Resources
Find proteins for O00408 (Homo sapiens) Explore O00408  Go to UniProtKB:  O00408
PHAROS:  O00408 GTEx:  ENSG00000186642

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
788	E [auth A], H [auth B], K [auth C], N [auth D]	N-benzyl-4-methyl-1-phenyl[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide C24 H19 N5 O HIUJNBXYERGONS-UHFFFAOYSA-N
ZN	F [auth A], I [auth B], L [auth C], O [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.277 
• R-Value Work: 0.206 
• R-Value Observed: 0.210 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.14	α = 109.37
b = 73.43	β = 91.82
c = 91.62	γ = 91.05

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Buijnsters, P., Andres, J.I., DeAngelis, M., Langlois, X., Rombouts, F., Sanderson, W., Tresadern, G., Trabanco, A., VanHoof, G., VanRoosbroeck, Y.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-09-24
  Changes: Database references
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description