6B96 image
Deposition Date 2017-10-10
Release Date 2017-11-22
Last Version Date 2024-03-06
Entry Detail
PDB ID:
6B96
Keywords:
HYDROLASE
Title:
Crystal Structure of PDE2 in complex with compound 16
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Spodoptera frugiperda
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.88 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
6B96 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:cGMP-dependent 3',5'-cyclic phosphodiesterase
Gene (Uniprot):PDE2A
Chain IDs:A, B
Chain Length:373
Number of Molecules:2
Biological Source:Homo sapiens
UniProt ID:O00408 Pfam ID:PF00233 EC:3.1.4.17
Ligand Molecules
CZV
EDO
MG
ZN
Primary Citation
The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design.
Bioorg. Med. Chem. Lett. 27 5167 5171 (2017)
PMID: 29113762 DOI: 10.1016/j.bmcl.2017.10.054

Abstact

We have identified a novel PDE2 inhibitor series using fragment-based screening. Pyrazolopyrimidine fragment 1, while possessing weak potency (Ki = 22.4 μM), exhibited good binding efficiencies (LBE = 0.49, LLE = 4.48) to serve as a start for structure-based drug design. With the assistance of molecular modeling and X-ray crystallography, this fragment was developed into a series of potent PDE2 inhibitors with good physicochemical properties. Compound 16, a PDE2 selective inhibitor, was identified that exhibited favorable rat pharmacokinetic properties.

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Primary Citation of related structures
6B96