4D08 | pdb_00004d08

PDE2a catalytic domain in complex with a brain penetrant inhibitor

PDB DOI: https://doi.org/10.2210/pdb4D08/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.247 (Depositor), 0.263 (DCC)
R-Value Work:
0.213 (Depositor)
R-Value Observed:
0.215 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ml500262u
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 167.82 kDa
Atom Count: 11,498
Modeled Residue Count: 1,338
Deposited Residue Count: 1,412
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q2T Query on Q2T Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], L [auth C], O [auth D]	1-(5-butoxypyridin-3-yl)-4-methyl-8-(morpholin-4-ylmethyl)[1,2,4]triazolo[4,3-a]quinoxaline C₂₄ H₂₈ N₆ O₂ JJQZDOKXARNTKH-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.247 (Depositor), 0.263 (DCC)
R-Value Work: 0.213 (Depositor)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.04	α = 109.04
b = 74.15	β = 91.73
c = 92.77	γ = 91.34

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Revision History (Full details and data files)

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