ISDA

Deposition Date 2017-10-10

Release Date 2017-11-22

Last Version Date 2024-03-06

Entry Detail

PDB ID:

6B97

Keywords:

HYDROLASE

Title:

Crystal structure of PDE2 in complex with complex 9

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Spodoptera frugiperda

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.76 Å

R-Value Free:

0.22

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 21 21 21

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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

CZY

EDO

Primary Citation

The identification of a novel lead class for phosphodiesterase 2 inhibition by fragment-based drug design.

Forster, A.B, Abeywickrema, P, Bunda, J, Cox, C.D, Cabalu, T.D, Egbertson, M, Fay, J, Getty, K, Hall, D, Kornienko, M, Lu, J, Parthasarathy, G, Reid, J, Sharma, S, Shipe, W.D, Smith, S.M, Soisson, S, Stachel, S.J, Su, H.P, Wang, D, Berger, R.Show

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