6CYD | pdb_00006cyd

PDE2 in complex with compound 7

• PDB DOI: https://doi.org/10.2210/pdb6CYD/pdb

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


• Deposited: 2018-04-05 Released: 2018-09-19 
• Deposition Author(s): Lu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Structure-Guided Design and Procognitive Assessment of a Potent and Selective Phosphodiesterase 2A Inhibitor.

Stachel, S.J., Berger, R., Nomland, A.B., Ginnetti, A.T., Paone, D.V., Wang, D., Puri, V., Lange, H., Drott, J., Lu, J., Marcus, J., Dwyer, M.P., Suon, S., Uslaner, J.M., Smith, S.M.

(2018) ACS Med Chem Lett 9: 815-820

• PubMed: 30128073 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00214
• Primary Citation of Related Structures:  
  6CYB, 6CYC, 6CYD


• PubMed Abstract: 
  

  Herein we describe the development of a series of pyrazolopyrimidinone phosphodiesterase 2A (PDE2) inhibitors using structure-guided lead identification and design. The series was derived from informed chemotype replacement based on previously identified internal leads. The initially designed compound 3 , while potent on PDE2, displayed unsatisfactory selectivity against the other PDE2 isoforms. Compound 3 was subsequently optimized for improved PDE2 activity and isoform selectivity. Insights into the origins of PDE2 selectivity are described and verified using cocrystallography. An optimized lead, 4 , demonstrated improved performance in both a rodent and a nonhuman primate cognition model.

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Organizational Affiliation: 

Merck & Co. Inc., P.O. Box 4, West Point, Pennsylvania 19486, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.46 kDa 
• Atom Count: 6,044 
• Modelled Residue Count: 691 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent 3',5'-cyclic phosphodiesterase	A, B	373	Homo sapiens	Mutation(s): 0  Gene Names: PDE2A 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FKG (Subject of Investigation/LOI)	E [auth A], J [auth B]	3-(hydroxymethyl)-6-methyl-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one C16 H15 F3 N4 O2 WOPONWMJGIDXSF-QMMMGPOBSA-N
ZN	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.94	α = 90
b = 91.82	β = 90
c = 102.83	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Lu, J.

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description