Fluorine in PDB 5sqo: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5030903496 - (R) Isomer

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5030903496 - (R) Isomer:
3.4.19.121;

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5030903496 - (R) Isomer, PDB code: 5sqo 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)	39.73 / 1.05
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	88.839, 88.839, 39.541, 90, 90, 90
R / Rfree (%)	14.4 / 16.2

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5030903496 - (R) Isomer (pdb code 5sqo). 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 Z5030903496 - (R) Isomer, PDB code: 5sqo:
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 Z5030903496 - (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 Z5030903496 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:13.5 occ:0.32 F14 A:QTF201 0.0 13.5 0.3 O A:HOH535 0.9 35.3 0.7 C11 A:QTF201 1.3 13.2 0.3 O A:HOH449 1.8 16.4 0.7 C10 A:QTF201 2.3 12.8 0.3 C12 A:QTF201 2.4 13.4 0.3 H101 A:QTF201 2.5 15.3 0.3 H121 A:QTF201 2.6 16.1 0.3 HB2 A:ALA52 2.6 15.4 0.7 HB2 A:ALA52 2.7 15.8 0.3 O A:HOH528 2.8 52.5 1.0 O A:HOH459 3.2 38.1 0.7 O A:HOH527 3.2 36.9 0.7 HB1 A:ALA52 3.4 15.8 0.3 CB A:ALA52 3.5 13.2 0.3 CB A:ALA52 3.5 12.8 0.7 C09 A:QTF201 3.6 13.0 0.3 C13 A:QTF201 3.6 13.5 0.3 HB1 A:ALA52 3.7 15.4 0.7 O A:HOH525 3.7 33.0 0.7 O A:HOH512 3.9 38.1 0.3 HB3 A:ALA52 3.9 15.8 0.3 HB3 A:ALA52 4.0 15.4 0.7 C08 A:QTF201 4.2 13.3 0.3 HA A:ALA52 4.4 13.1 0.7 O A:GLY48 4.4 11.8 0.7 H131 A:QTF201 4.5 16.2 0.3 CA A:ALA52 4.5 10.9 0.7 HA A:ALA52 4.5 15.2 0.3 O A:GLY48 4.5 15.0 0.3 CA A:ALA52 4.6 12.7 0.3 H A:ALA52 4.7 12.2 0.7 HA A:VAL49 4.8 16.9 0.3 HZ A:PHE156 4.8 24.9 0.3 N15 A:QTF201 4.8 12.8 0.3 N A:ALA52 4.9 10.2 0.7 H A:ALA52 5.0 15.0 0.3 CZ A:PHE156 5.0 20.8 0.3

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z5030903496 - (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 Z5030903496 - (R) Isomer within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:17.0 occ:0.32 F25 A:QTF201 0.0 17.0 0.3 C03 A:QTF201 1.3 16.6 0.3 HA3 A:GLY130 1.5 16.6 0.7 O A:HOH517 1.6 34.0 0.7 O A:HOH447 2.2 16.2 0.7 C21 A:QTF201 2.3 16.5 0.3 CA A:GLY130 2.4 13.8 0.7 C04 A:QTF201 2.4 16.0 0.3 C02 A:QTF201 2.4 17.1 0.3 O A:HOH497 2.4 33.9 0.7 HA3 A:GLY130 2.5 19.2 0.3 H042 A:QTF201 2.6 19.2 0.3 HA2 A:GLY130 2.6 16.6 0.7 O01 A:QTF201 2.7 17.4 0.3 H241 A:QTF201 2.8 20.2 0.3 C24 A:QTF201 2.9 16.8 0.3 C20 A:QTF201 3.0 16.3 0.3 H201 A:QTF201 3.0 19.6 0.3 N05 A:QTF201 3.0 15.6 0.3 N A:GLY130 3.0 13.2 0.7 H242 A:QTF201 3.2 20.2 0.3 H A:ILE131 3.2 15.5 0.7 H041 A:QTF201 3.3 19.2 0.3 H A:GLY130 3.4 15.8 0.7 CA A:GLY130 3.4 16.0 0.3 O26 A:QTF201 3.4 17.4 0.3 H A:ILE131 3.5 18.9 0.3 C A:GLY130 3.5 13.0 0.7 C A:ALA129 3.6 11.5 0.7 O A:HOH495 3.7 43.5 1.0 N A:ILE131 3.7 12.9 0.7 C22 A:QTF201 3.7 16.1 0.3 O A:ALA129 3.8 11.5 0.7 HA2 A:GLY130 3.8 19.2 0.3 O A:HOH531 4.0 31.7 0.7 N A:GLY130 4.0 15.7 0.3 H202 A:QTF201 4.0 19.6 0.3 H222 A:QTF201 4.0 19.2 0.3 O A:HOH450 4.1 13.5 0.7 O A:HOH341 4.1 19.1 0.7 C23 A:QTF201 4.1 16.5 0.3 HG23 A:VAL49 4.1 17.6 0.7 N A:ILE131 4.2 15.8 0.3 O A:ALA129 4.2 15.4 0.3 HG12 A:ILE131 4.2 23.2 0.3 C A:ALA129 4.3 15.1 0.3 H131 A:QTF201 4.3 16.2 0.3 C A:GLY130 4.3 16.0 0.3 HB3 A:ALA129 4.4 15.8 0.7 O A:HOH419 4.4 12.8 0.7 C06 A:QTF201 4.5 14.4 0.3 H221 A:QTF201 4.5 19.2 0.3 H A:GLY130 4.5 18.8 0.3 O A:HOH506 4.5 46.3 1.0 HB1 A:ALA129 4.5 15.8 0.7 HG23 A:ILE131 4.6 18.9 0.7 O A:GLY130 4.7 13.0 0.7 O A:HOH432 4.7 26.3 0.7 O A:HOH464 4.7 18.0 0.7 HG23 A:ILE131 4.7 21.7 0.3 H231 A:QTF201 4.8 19.7 0.3 CB A:ALA129 4.8 13.2 0.7 HG12 A:ILE131 4.8 19.5 0.7 CA A:ALA129 4.8 12.1 0.7 H A:VAL49 4.8 12.8 0.7 HB3 A:ALA129 4.9 17.6 0.3 H232 A:QTF201 4.9 19.7 0.3 H A:PHE132 5.0 14.1 0.7 HA2 A:GLY48 5.0 14.6 0.7 O A:HOH329 5.0 23.4 1.0 HD1 A:PHE132 5.0 21.8 0.3

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