Fluorine in PDB 7far: Crystal Structure of PDE5A in Complex with Inhibitor L12

All present enzymatic activity of Crystal Structure of PDE5A in Complex with Inhibitor L12:
3.1.4.35;

The structure of Crystal Structure of PDE5A in Complex with Inhibitor L12, PDB code: 7far was solved by D.Wu, Y.Y.Huang, H.B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.80 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	73.917, 73.917, 132.251, 90, 90, 120
R / Rfree (%)	21.3 / 25

The structure of Crystal Structure of PDE5A in Complex with Inhibitor L12 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of PDE5A in Complex with Inhibitor L12 (pdb code 7far). 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 PDE5A in Complex with Inhibitor L12, PDB code: 7far:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of PDE5A in Complex with Inhibitor L12


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 PDE5A in Complex with Inhibitor L12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:52.4 occ:1.00 F31 A:2VI903 0.0 52.4 1.0 C29 A:2VI903 1.3 45.5 1.0 F30 A:2VI903 1.7 54.3 1.0 O10 A:2VI903 2.1 46.6 1.0 OE1 A:GLN775 2.8 39.8 1.0 C3 A:2VI903 3.2 49.4 1.0 CB A:ALA779 3.4 35.1 1.0 CA A:ALA779 3.5 40.4 1.0 N A:ALA779 3.5 39.3 1.0 CD A:GLN775 3.5 40.8 1.0 O A:GLN775 3.6 43.0 1.0 CG A:GLN775 3.6 40.3 1.0 C2 A:2VI903 4.0 44.9 1.0 CD1 A:ILE768 4.2 33.2 1.0 C4 A:2VI903 4.2 48.8 1.0 OE1 A:GLN817 4.3 37.4 1.0 C A:ILE778 4.4 39.4 1.0 CB A:ILE778 4.5 41.6 1.0 N7 A:2VI903 4.6 49.6 1.0 C A:GLN775 4.6 41.1 1.0 NE2 A:GLN817 4.7 46.6 1.0 CG2 A:ILE778 4.7 42.1 1.0 NE2 A:GLN775 4.8 41.4 1.0 CD A:GLN817 4.8 45.7 1.0 CG2 A:VAL782 4.8 38.3 1.0 O A:ALA767 4.9 33.2 1.0 CB A:ALA767 4.9 32.8 1.0 CB A:GLN775 4.9 39.8 1.0 CA A:ILE768 4.9 37.0 1.0 C A:ALA779 4.9 41.3 1.0 C A:ALA767 5.0 37.3 1.0 CA A:GLN775 5.0 39.8 1.0 O A:ILE778 5.0 45.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of PDE5A in Complex with Inhibitor L12


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 PDE5A in Complex with Inhibitor L12 within 5.0Å range: probe atom residue distance (Å) B Occ A:F903 b:54.3 occ:1.00 F30 A:2VI903 0.0 54.3 1.0 C29 A:2VI903 1.3 45.5 1.0 F31 A:2VI903 1.7 52.4 1.0 O10 A:2VI903 2.1 46.6 1.0 C3 A:2VI903 2.6 49.4 1.0 C2 A:2VI903 2.8 44.9 1.0 CG2 A:ILE778 3.5 42.1 1.0 CB A:ALA767 3.7 32.8 1.0 CG2 A:VAL782 3.8 38.3 1.0 N A:ALA779 3.8 39.3 1.0 CB A:ILE778 3.8 41.6 1.0 C4 A:2VI903 3.8 48.8 1.0 CA A:ALA779 4.0 40.4 1.0 C1 A:2VI903 4.1 46.1 1.0 C A:ILE778 4.1 39.4 1.0 OE1 A:GLN775 4.5 39.8 1.0 O A:GLN775 4.5 43.0 1.0 C A:ALA767 4.6 37.3 1.0 O A:ILE778 4.6 45.1 1.0 CB A:ALA779 4.6 35.1 1.0 CA A:ILE778 4.6 41.6 1.0 N A:ILE768 4.7 36.3 1.0 N7 A:2VI903 4.7 49.6 1.0 CG A:GLN775 4.7 40.3 1.0 CB A:VAL782 4.7 40.3 1.0 O A:ALA767 4.8 33.2 1.0 CA A:ALA767 4.8 33.7 1.0 C5 A:2VI903 4.9 49.6 1.0 CG1 A:ILE778 5.0 40.4 1.0 CD A:GLN775 5.0 40.8 1.0 CD1 A:ILE768 5.0 33.2 1.0

D.Wu, X.Zheng, R.Liu, Z.Li, Z.Jiang, Q.Zhou, Y.Huang, X.N.Wu, C.Zhang, Y.Y.Huang, H.B.Luo. Free Energy Perturbation (Fep)-Guided Scaffold Hopping. Acta Pharm Sin B V. 12 1351 2022.
ISSN: ISSN 2211-3835
PubMed: 35530128
DOI: 10.1016/J.APSB.2021.09.027