Fluorine in PDB 5we9: Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731), PDB code: 5we9 was solved by G.Kumar, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.57 / 1.80
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	74.081, 74.081, 127.694, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 22.6

The structure of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) (pdb code 5we9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731), PDB code: 5we9:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)


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 Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:32.7 occ:0.44 F1 A:GY7303 0.0 32.7 0.4 C1 A:GY7303 1.4 27.4 0.4 F2 A:GY7303 1.7 33.2 0.6 O1 A:GY7303 2.0 23.3 0.6 C3 A:GY7303 2.1 21.4 0.6 C21 A:GY7303 2.2 22.2 0.6 C24 A:GY7303 2.3 25.7 0.4 C2 A:GY7303 2.4 27.2 0.6 C2 A:GY7303 2.4 25.1 0.4 C3 A:GY7303 2.9 23.0 0.4 N1 A:GY7303 2.9 24.2 0.6 N2 A:GY7303 3.0 8.6 0.6 O1 A:GY7303 3.1 26.1 0.4 N3 A:GY7303 3.2 17.3 0.6 C22 A:GY7303 3.5 14.7 0.6 N3 A:GY7303 3.5 15.2 0.4 N2 A:GY7303 3.6 9.2 0.4 C23 A:GY7303 3.6 17.4 0.4 C21 A:GY7303 3.6 27.5 0.4 C5 A:GY7303 3.6 13.5 0.6 C6 A:GY7303 3.6 9.7 0.6 C1 A:GY7303 3.7 30.8 0.6 N1 A:GY7303 3.7 25.4 0.4 C7 A:GY7303 3.8 13.5 0.6 C4 A:GY7303 3.8 19.9 0.6 C20 A:GY7303 3.9 26.4 0.6 C6 A:GY7303 4.0 7.6 0.4 C7 A:GY7303 4.0 14.2 0.4 C8 A:GY7303 4.0 24.6 0.4 C8 A:GY7303 4.1 24.5 0.6 C22 A:GY7303 4.1 30.1 0.4 O A:HOH496 4.2 33.1 1.0 C5 A:GY7303 4.2 12.3 0.4 F1 A:GY7303 4.4 29.5 0.6 C23 A:GY7303 4.5 25.5 0.6 C20 A:GY7303 4.5 29.1 0.4 C4 A:GY7303 4.5 20.3 0.4 C24 A:GY7303 4.6 27.0 0.6 C15 A:GY7303 4.6 41.9 0.6 CG1 A:ILE38 4.7 11.5 1.0 N4 A:GY7303 4.7 11.8 0.6 F2 A:GY7303 4.7 34.4 0.4 C16 A:GY7303 4.7 9.7 0.6 C10 A:GY7303 4.8 39.5 0.6 C19 A:GY7303 4.8 26.9 0.6 O2 A:GY7303 4.8 14.1 0.6 C15 A:GY7303 4.8 42.0 0.4 O A:HOH416 4.9 21.6 1.0 C16 A:GY7303 4.9 9.2 0.4 O2 A:GY7303 4.9 10.5 0.4 C14 A:GY7303 4.9 42.4 0.6 CD1 A:ILE38 5.0 14.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)


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 Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:29.5 occ:0.56 F1 A:GY7303 0.0 29.5 0.6 C1 A:GY7303 1.4 30.8 0.6 O1 A:GY7303 2.2 26.1 0.4 C24 A:GY7303 2.3 27.0 0.6 C2 A:GY7303 2.4 27.2 0.6 C3 A:GY7303 2.8 21.4 0.6 C3 A:GY7303 3.2 23.0 0.4 CD A:LYS34 3.4 40.7 1.0 O1 A:GY7303 3.4 23.3 0.6 CG A:LYS34 3.4 34.9 1.0 N1 A:GY7303 3.5 24.2 0.6 CD1 A:ILE38 3.5 14.8 1.0 C23 A:GY7303 3.6 25.5 0.6 C21 A:GY7303 3.6 22.2 0.6 C2 A:GY7303 3.7 25.1 0.4 CG1 A:ILE38 3.8 11.5 1.0 C20 A:GY7303 3.9 26.4 0.6 C22 A:GY7303 4.1 14.7 0.6 C21 A:GY7303 4.3 27.5 0.4 N1 A:GY7303 4.3 25.4 0.4 C1 A:GY7303 4.3 27.4 0.4 F2 A:GY7303 4.4 34.4 0.4 F1 A:GY7303 4.4 32.7 0.4 CE A:LYS34 4.5 40.7 1.0 C4 A:GY7303 4.6 19.9 0.6 OE2 A:GLU26 4.6 43.1 1.0 F2 A:GY7303 4.7 33.2 0.6 C20 A:GY7303 4.9 29.1 0.4 CB A:LYS34 4.9 20.6 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:34.4 occ:0.44 F2 A:GY7303 0.0 34.4 0.4 C21 A:GY7303 1.4 27.5 0.4 C4 A:GY7303 2.0 19.9 0.6 C22 A:GY7303 2.3 30.1 0.4 C2 A:GY7303 2.4 25.1 0.4 N1 A:GY7303 2.8 24.2 0.6 C3 A:GY7303 2.8 23.0 0.4 C18 A:GY7303 2.9 27.5 0.6 C5 A:GY7303 2.9 13.5 0.6 O1 A:GY7303 3.0 23.3 0.6 C4 A:GY7303 3.0 20.3 0.4 C3 A:GY7303 3.2 21.4 0.6 N1 A:GY7303 3.2 25.4 0.4 N4 A:GY7303 3.2 11.8 0.6 O A:HOH500 3.5 32.2 1.0 C5 A:GY7303 3.6 12.3 0.4 C23 A:GY7303 3.6 17.4 0.4 C1 A:GY7303 3.6 27.4 0.4 O1 A:GY7303 3.6 26.1 0.4 N4 A:GY7303 3.7 9.2 0.4 C20 A:GY7303 3.9 26.4 0.6 N2 A:GY7303 4.0 8.6 0.6 C19 A:GY7303 4.1 26.9 0.6 C24 A:GY7303 4.1 25.7 0.4 O A:HOH445 4.2 30.3 1.0 C18 A:GY7303 4.3 27.4 0.4 F1 A:GY7303 4.4 29.5 0.6 N2 A:GY7303 4.5 9.2 0.4 C17 A:GY7303 4.5 12.6 0.6 C2 A:GY7303 4.5 27.2 0.6 C20 A:GY7303 4.6 29.1 0.4 O A:HOH415 4.6 14.9 1.0 F1 A:GY7303 4.7 32.7 0.4 OH A:TYR130 4.7 41.5 1.0 C17 A:GY7303 4.8 10.9 0.4 NH2 A:ARG124 4.9 38.1 1.0 C1 A:GY7303 5.0 30.8 0.6

Fluorine binding site 4 out of 4 in the Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Influenza Virus Pa Endonuclease in Complex with Inhibitor 7B (Sri-29731) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:33.2 occ:0.56 F2 A:GY7303 0.0 33.2 0.6 C21 A:GY7303 1.4 22.2 0.6 F1 A:GY7303 1.7 32.7 0.4 C22 A:GY7303 2.3 14.7 0.6 C2 A:GY7303 2.4 27.2 0.6 C3 A:GY7303 2.8 21.4 0.6 C1 A:GY7303 3.0 27.4 0.4 C15 A:GY7303 3.0 41.9 0.6 N3 A:GY7303 3.0 17.3 0.6 N3 A:GY7303 3.2 15.2 0.4 O1 A:GY7303 3.3 26.1 0.4 C15 A:GY7303 3.3 42.0 0.4 C8 A:GY7303 3.3 24.6 0.4 C3 A:GY7303 3.4 23.0 0.4 C8 A:GY7303 3.4 24.5 0.6 C14 A:GY7303 3.4 42.4 0.6 O1 A:GY7303 3.4 23.3 0.6 N1 A:GY7303 3.4 24.2 0.6 C10 A:GY7303 3.5 39.5 0.6 C2 A:GY7303 3.6 25.1 0.4 C23 A:GY7303 3.6 25.5 0.6 C1 A:GY7303 3.6 30.8 0.6 C20 A:GY7303 3.7 26.4 0.6 N2 A:GY7303 3.7 8.6 0.6 C10 A:GY7303 3.8 39.4 0.4 C14 A:GY7303 3.8 42.0 0.4 N1 A:GY7303 3.9 25.4 0.4 C9 A:GY7303 4.0 33.1 0.6 C24 A:GY7303 4.0 25.7 0.4 C9 A:GY7303 4.1 32.9 0.4 N2 A:GY7303 4.1 9.2 0.4 C7 A:GY7303 4.1 13.5 0.6 C24 A:GY7303 4.1 27.0 0.6 C20 A:GY7303 4.1 29.1 0.4 C13 A:GY7303 4.2 42.8 0.6 C7 A:GY7303 4.2 14.2 0.4 C11 A:GY7303 4.3 38.8 0.6 C6 A:GY7303 4.4 9.7 0.6 C12 A:GY7303 4.6 39.2 0.6 C6 A:GY7303 4.6 7.6 0.4 C4 A:GY7303 4.6 19.9 0.6 C5 A:GY7303 4.6 13.5 0.6 C11 A:GY7303 4.6 37.5 0.4 O A:HOH518 4.6 44.2 1.0 C13 A:GY7303 4.7 40.7 0.4 F1 A:GY7303 4.7 29.5 0.6 C19 A:GY7303 4.7 26.9 0.6 C5 A:GY7303 4.9 12.3 0.4 C21 A:GY7303 5.0 27.5 0.4

D.Beylkin, G.Kumar, W.Zhou, J.Park, T.Jeevan, C.Lagisetti, R.Harfoot, R.J.Webby, S.W.White, T.R.Webb. Protein-Structure Assisted Optimization of 4,5-Dihydroxypyrimidine-6-Carboxamide Inhibitors of Influenza Virus Endonuclease. Sci Rep V. 7 17139 2017.
ISSN: ESSN 2045-2322
PubMed: 29215062
DOI: 10.1038/S41598-017-17419-6