Fluorine in PDB 5sr6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer, PDB code: 5sr6 was solved by G.J.Correy, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.762, 88.762, 39.582, 90, 90, 90
R / Rfree (%)	13.6 / 15.3

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer (pdb code 5sr6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer, PDB code: 5sr6:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:15.5 occ:0.14 F1 A:QZF201 0.0 15.5 0.1 H9 A:QZF202 0.8 19.4 0.1 C2 A:QZF201 1.4 15.5 0.1 C14 A:QZF202 1.6 16.2 0.1 O A:HOH541 1.7 28.2 0.8 HA3 A:GLY130 1.7 14.8 0.8 O1 A:QZF202 2.2 17.1 0.1 C15 A:QZF202 2.2 16.6 0.1 C1 A:QZF202 2.2 17.0 0.1 HA3 A:GLY130 2.3 18.5 0.2 C3 A:QZF201 2.3 15.2 0.1 H2 A:QZF201 2.3 18.2 0.1 C15 A:QZF201 2.3 15.5 0.1 C1 A:QZF201 2.4 15.5 0.1 H10 A:QZF202 2.4 19.4 0.1 H16 A:QZF202 2.4 19.9 0.1 O A:HOH516 2.4 34.7 0.8 CA A:GLY130 2.5 12.3 0.8 N1 A:QZF202 2.5 15.8 0.1 O A:HOH444 2.5 14.2 0.8 H12 A:QZF201 2.6 18.9 0.1 C18 A:QZF202 2.6 16.6 0.1 C2 A:QZF202 2.6 16.9 0.1 HA2 A:GLY130 2.7 14.8 0.8 O1 A:QZF201 2.7 15.4 0.1 H10 A:QZF201 2.7 18.2 0.1 C16 A:QZF201 2.8 15.7 0.1 C14 A:QZF201 2.9 15.1 0.1 O A:HOH336 2.9 41.9 1.0 O2 A:QZF202 3.0 17.1 0.1 H15 A:QZF202 3.0 19.9 0.1 N1 A:QZF201 3.0 14.6 0.1 H1 A:QZF201 3.1 18.2 0.1 N A:GLY130 3.1 11.9 0.8 CA A:GLY130 3.2 15.4 0.2 C3 A:QZF202 3.2 16.3 0.1 H11 A:QZF201 3.3 18.9 0.1 H A:GLY130 3.4 14.2 0.8 H A:ILE131 3.4 14.0 0.8 O2 A:QZF201 3.5 15.7 0.1 HA2 A:GLY130 3.5 18.5 0.2 H A:ILE131 3.6 18.9 0.2 C4 A:QZF202 3.6 14.8 0.1 N4 A:QZF202 3.6 14.6 0.1 C16 A:QZF202 3.7 16.4 0.1 C A:ALA129 3.7 10.6 0.8 N A:GLY130 3.7 15.4 0.2 C A:GLY130 3.7 11.8 0.8 H1 A:QZF202 3.8 19.6 0.1 C18 A:QZF201 3.8 15.4 0.1 H9 A:QZF201 3.8 18.2 0.1 O A:HOH547 3.8 41.0 0.8 O A:ALA129 3.8 10.6 0.8 F1 A:QZF202 3.9 17.3 0.1 C17 A:QZF202 3.9 16.6 0.1 N A:ILE131 3.9 11.7 0.8 H2 A:QZF202 3.9 19.6 0.1 O A:HOH340 4.0 18.0 0.8 H11 A:QZF202 4.0 19.7 0.1 C17 A:QZF201 4.1 15.7 0.1 H A:GLY130 4.1 18.5 0.2 H16 A:QZF201 4.1 18.5 0.1 O A:ALA129 4.1 15.7 0.2 HG23 A:VAL49 4.1 16.1 0.8 C A:ALA129 4.1 15.2 0.2 O A:HOH474 4.2 50.8 1.0 N A:ILE131 4.2 15.8 0.2 O A:HOH453 4.2 11.8 0.8 O A:HOH507 4.2 38.3 0.9 C A:GLY130 4.2 15.7 0.2 H14 A:QZF202 4.2 19.9 0.1 HB3 A:ALA129 4.3 14.9 0.8 H12 A:QZF202 4.3 19.7 0.1 H13 A:QZF201 4.4 18.8 0.1 C4 A:QZF201 4.4 13.6 0.1 H6 A:QZF201 4.4 15.7 0.1 HB1 A:ALA129 4.4 14.9 0.8 H15 A:QZF201 4.5 18.5 0.1 O A:HOH419 4.5 11.8 0.8 HB3 A:ALA129 4.5 17.1 0.2 HG12 A:ILE131 4.5 21.4 0.2 O A:HOH469 4.5 23.3 0.8 H13 A:QZF202 4.6 19.9 0.1 O A:HOH310 4.7 25.8 1.0 CB A:ALA129 4.7 12.4 0.8 HG23 A:ILE131 4.8 16.9 0.8 CA A:ALA129 4.8 11.0 0.8 O A:GLY130 4.8 12.2 0.8 H14 A:QZF201 4.8 18.8 0.1 C13 A:QZF202 4.8 14.4 0.1 O A:HOH454 4.9 24.9 0.9 H A:VAL49 4.9 12.3 0.8 C5 A:QZF202 4.9 14.2 0.1 CG2 A:VAL49 5.0 13.4 0.8 HG12 A:ILE131 5.0 18.0 0.8

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z3011799020 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:17.3 occ:0.10 F1 A:QZF202 0.0 17.3 0.1 H9 A:QZF201 0.8 18.2 0.1 C14 A:QZF201 1.2 15.1 0.1 H10 A:QZF201 1.3 18.2 0.1 C2 A:QZF202 1.4 16.9 0.1 O A:HOH516 1.6 34.7 0.8 N1 A:QZF201 2.2 14.6 0.1 O A:HOH340 2.3 18.0 0.8 C3 A:QZF202 2.4 16.3 0.1 C15 A:QZF202 2.4 16.6 0.1 HB2 A:PRO125 2.4 16.1 0.2 C1 A:QZF202 2.4 17.0 0.1 N4 A:QZF201 2.4 13.4 0.1 O A:HOH469 2.5 23.3 0.8 C15 A:QZF201 2.5 15.5 0.1 H2 A:QZF202 2.5 19.6 0.1 HB2 A:PRO125 2.5 13.0 0.8 H12 A:QZF202 2.6 19.7 0.1 HG21 A:VAL49 2.7 16.1 0.8 H1 A:QZF202 2.7 19.6 0.1 C4 A:QZF201 2.7 13.6 0.1 H15 A:QZF201 2.9 18.5 0.1 C16 A:QZF202 2.9 16.4 0.1 H A:LEU126 2.9 16.8 0.2 H11 A:QZF201 3.0 18.9 0.1 O A:HOH426 3.0 21.0 0.9 O A:HOH311 3.0 18.6 1.0 O1 A:QZF202 3.1 17.1 0.1 HG23 A:VAL49 3.1 16.1 0.8 H15 A:QZF202 3.1 19.9 0.1 HB3 A:PRO125 3.2 13.0 0.8 CB A:PRO125 3.2 13.4 0.2 O2 A:QZF202 3.2 17.1 0.1 C18 A:QZF201 3.2 15.4 0.1 CB A:PRO125 3.2 10.8 0.8 CG2 A:VAL49 3.2 13.4 0.8 C16 A:QZF201 3.3 15.7 0.1 HB3 A:PRO125 3.3 16.1 0.2 C18 A:QZF202 3.3 16.6 0.1 C3 A:QZF201 3.4 15.2 0.1 C2 A:QZF201 3.5 15.5 0.1 HG22 A:VAL49 3.5 16.1 0.8 O A:HOH507 3.5 38.3 0.9 N1 A:QZF202 3.5 15.8 0.1 C14 A:QZF202 3.5 16.2 0.1 H A:LEU126 3.6 12.7 0.8 N A:LEU126 3.6 14.0 0.2 C13 A:QZF201 3.6 13.4 0.1 C17 A:QZF202 3.7 16.6 0.1 H11 A:QZF202 3.7 19.7 0.1 H13 A:QZF202 3.8 19.9 0.1 C17 A:QZF201 3.9 15.7 0.1 H8 A:QZF201 3.9 16.0 0.1 O A:HOH541 3.9 28.2 0.8 F1 A:QZF201 3.9 15.5 0.1 H14 A:QZF201 4.0 18.8 0.1 H2 A:QZF201 4.0 18.2 0.1 HA A:PRO125 4.0 15.9 0.2 H16 A:QZF201 4.0 18.5 0.1 H1 A:QZF201 4.0 18.2 0.1 HA A:PRO125 4.0 12.5 0.8 CA A:PRO125 4.0 13.3 0.2 H9 A:QZF202 4.0 19.4 0.1 H12 A:QZF201 4.1 18.9 0.1 HB3 A:LEU126 4.1 18.0 0.2 HB3 A:ALA129 4.1 14.9 0.8 CA A:PRO125 4.1 10.4 0.8 C5 A:QZF201 4.1 13.1 0.1 N A:LEU126 4.1 10.6 0.8 H16 A:QZF202 4.1 19.9 0.1 O A:LEU126 4.2 14.3 0.2 H10 A:QZF202 4.2 19.4 0.1 C A:PRO125 4.2 13.6 0.2 HB A:VAL49 4.3 16.8 0.2 O A:LEU126 4.3 11.5 0.8 HG11 A:VAL49 4.3 17.1 0.2 H6 A:QZF202 4.3 16.4 0.1 O A:HOH547 4.3 41.0 0.8 CG A:PRO125 4.4 13.5 0.2 HB2 A:LEU126 4.5 13.8 0.8 CG A:PRO125 4.5 11.0 0.8 HG2 A:PRO125 4.5 16.2 0.2 CA A:LEU126 4.5 14.3 0.2 C A:PRO125 4.6 10.3 0.8 HG3 A:PRO125 4.6 16.2 0.2 HG3 A:PRO125 4.6 13.2 0.8 H A:PHE156 4.6 19.5 0.2 H14 A:QZF202 4.6 19.9 0.1 O A:ALA154 4.6 13.7 0.8 C A:LEU126 4.6 13.9 0.2 CB A:VAL49 4.6 11.6 0.8 CB A:LEU126 4.7 15.0 0.2 HG2 A:PRO125 4.7 13.2 0.8 O A:ALA154 4.7 14.0 0.2 HB2 A:LEU126 4.7 18.0 0.2 HB A:VAL49 4.8 13.9 0.8 O A:HOH419 4.8 11.8 0.8 H A:PHE156 4.8 22.9 0.8 H13 A:QZF201 4.8 18.8 0.1 N3 A:QZF201 4.8 13.2 0.1 C1 A:QZF201 4.8 15.5 0.1 HG21 A:VAL49 4.8 16.6 0.2 HA A:VAL155 4.8 19.5 0.8 HG11 A:VAL49 4.8 15.1 0.8 O A:HOH454 4.9 24.9 0.9 C12 A:QZF201 4.9 13.0 0.1 C4 A:QZF202 4.9 14.8 0.1 HB2 A:PHE156 4.9 21.9 0.2 HB3 A:ALA129 4.9 17.1 0.2 HA A:VAL155 4.9 17.4 0.2 CG1 A:VAL49 5.0 14.2 0.2

S.Gahbauer, G.J.Correy, M.Schuller, M.P.Ferla, Y.U.Doruk, M.Rachman, T.Wu, M.Diolaiti, S.Wang, R.J.Neitz, D.Fearon, D.Radchenko, Y.Moroz, J.J.Irwin, A.R.Renslo, J.C.Taylor, J.E.Gestwicki, F.Von Delft, A.Ashworth, I.Ahel, B.K.Shoichet, J.S.Fraser. Structure-Based Inhibitor Optimization For the NSP3 Macrodomain of Sars-Cov-2. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 35794891
DOI: 10.1101/2022.06.27.497816