Fluorine in PDB 6a3n: Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2

All present enzymatic activity of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2:
3.1.4.35;

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n was solved by Y.N.Wu, Q.Zhou, Y.P.Chen, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.46 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.110, 104.110, 269.079, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 28

The structure of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 (pdb code 6a3n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2, PDB code: 6a3n:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:32.8 occ:1.00 F26 A:9Q9603 0.0 32.8 1.0 C24 A:9Q9603 1.4 33.3 1.0 C25 A:9Q9603 2.4 33.3 1.0 C23 A:9Q9603 2.4 33.8 1.0 N21 A:9Q9603 3.4 33.3 1.0 C22 A:9Q9603 3.5 33.8 1.0 C16 A:9Q9603 3.6 31.5 1.0 C17 A:9Q9603 4.1 31.5 1.0 C13 A:9Q9603 4.1 30.9 1.0 CB A:MET365 4.1 21.0 1.0 CG A:MET365 4.2 20.9 1.0 OH A:TYR424 4.2 29.3 1.0 CE1 A:PHE456 4.3 21.7 1.0 CE A:MET365 4.5 20.4 1.0 C1 A:9Q9603 4.6 32.3 1.0 O A:HOH736 4.7 18.9 1.0 N5 A:9Q9603 4.7 29.6 1.0 C18 A:9Q9603 4.8 31.0 1.0 CD1 A:PHE456 4.9 21.7 1.0 N10 A:9Q9603 5.0 30.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the PDE9 Catalytic Domain in Complex with Inhibitor 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F603 b:30.4 occ:1.00 F26 B:9Q9603 0.0 30.4 1.0 C24 B:9Q9603 1.4 31.0 1.0 C23 B:9Q9603 2.4 31.3 1.0 C25 B:9Q9603 2.4 30.0 1.0 C22 B:9Q9603 2.9 30.9 1.0 N21 B:9Q9603 3.1 30.3 1.0 C16 B:9Q9603 3.2 23.1 1.0 CG B:MET365 3.9 24.9 1.0 CE1 B:PHE456 4.0 22.2 1.0 C13 B:9Q9603 4.0 23.1 1.0 CB B:MET365 4.1 24.5 1.0 CE B:MET365 4.1 24.5 1.0 C1 B:9Q9603 4.3 29.7 1.0 C17 B:9Q9603 4.5 23.5 1.0 N5 B:9Q9603 4.6 23.9 1.0 CD1 B:PHE456 4.6 22.4 1.0 OH B:TYR424 4.6 27.7 1.0 SD B:MET365 4.8 25.0 1.0 N10 B:9Q9603 4.8 23.2 1.0 CZ B:PHE456 4.9 22.3 1.0 O B:HOH787 4.9 13.8 1.0 O B:HOH792 4.9 19.4 1.0

Y.Wu, Q.Zhou, T.Zhang, Z.Li, Y.P.Chen, P.Zhang, Y.F.Yu, H.Geng, Y.J.Tian, C.Zhang, Y.Wang, J.W.Chen, Y.Chen, H.B.Luo. Discovery of Potent, Selective, and Orally Bioavailable Inhibitors Against Phosphodiesterase-9, A Novel Target For the Treatment of Vascular Dementia. J. Med. Chem. V. 62 4218 2019.
ISSN: ISSN 1520-4804
PubMed: 30916555
DOI: 10.1021/ACS.JMEDCHEM.8B01041