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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.210 (Depositor), 0.217 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.8b00214
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00408
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FKG (Subject of Investigation/LOI) Query on FKG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	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		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.210 (Depositor), 0.217 (DCC)
R-Value Work: 0.182 (Depositor)
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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-09-19

Deposition Author(s):

Lu, J.

Revision History (Full details and data files)

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