Fluorine in PDB 7l7o: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49, PDB code: 7l7o was solved by J.Zephyr, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.94 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.133, 58.752, 59.731, 90, 90, 90
R / Rfree (%)	15 / 17

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49 (pdb code 7l7o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49, PDB code: 7l7o:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49


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 Hcv NS3/4A D168A Protease in Complex with NR04-49 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:23.0 occ:1.00 F54 A:XSY1202 0.0 23.0 1.0 C32 A:XSY1202 1.4 17.3 1.0 F55 A:XSY1202 2.2 25.4 1.0 F56 A:XSY1202 2.2 23.4 1.0 C25 A:XSY1202 2.3 14.8 1.0 HB2 A:ALA1156 2.7 13.0 1.0 HG2 A:ARG1155 2.7 19.9 0.7 O07 A:XSY1202 2.8 16.2 1.0 H011 A:XSY1202 2.9 15.1 1.0 C24 A:XSY1202 2.9 16.6 1.0 HH11 A:ARG1155 3.0 25.2 0.7 HG2 A:ARG1155 3.0 22.9 0.3 HG3 A:ARG1155 3.2 19.9 0.7 HD2 A:ARG1155 3.2 21.3 0.3 OD2 A:ASP1081 3.3 12.4 1.0 N30 A:XSY1202 3.3 23.3 1.0 CG A:ARG1155 3.3 16.6 0.7 O A:ARG1155 3.4 11.4 0.3 HD1 A:HIS1057 3.4 12.5 1.0 O A:ARG1155 3.5 11.5 0.7 CB A:ALA1156 3.6 10.8 1.0 NH1 A:ARG1155 3.7 21.0 0.7 C01 A:XSY1202 3.7 12.6 1.0 HD2 A:ARG1155 3.7 18.6 0.7 ND1 A:HIS1057 3.7 10.4 1.0 HE1 A:HIS1057 3.8 12.3 1.0 CG A:ARG1155 3.8 19.1 0.3 CD A:ARG1155 3.8 17.7 0.3 H022 A:XSY1202 3.9 15.2 1.0 HD3 A:ARG1155 3.9 21.3 0.3 CE1 A:HIS1057 3.9 10.3 1.0 C05 A:XSY1202 3.9 14.7 1.0 HH12 A:ARG1155 4.0 25.2 0.7 C A:ARG1155 4.0 11.6 0.3 HB1 A:ALA1156 4.0 13.0 1.0 C A:ARG1155 4.0 11.6 0.7 HB3 A:ALA1156 4.1 13.0 1.0 CD A:ARG1155 4.1 15.5 0.7 C02 A:XSY1202 4.1 12.7 1.0 N03 A:XSY1202 4.2 11.9 1.0 N26 A:XSY1202 4.2 23.7 1.0 H101 A:XSY1202 4.3 12.1 1.0 CG A:ASP1081 4.3 11.2 1.0 HA A:ALA1156 4.4 12.4 1.0 CA A:ALA1156 4.4 10.4 1.0 HG3 A:ARG1155 4.5 22.9 0.3 H492 A:XSY1202 4.5 26.5 1.0 C28 A:XSY1202 4.5 25.6 1.0 N A:ALA1156 4.5 11.2 1.0 CB A:ARG1155 4.6 13.9 0.7 H051 A:XSY1202 4.6 17.6 1.0 HB2 A:ASP1081 4.6 10.6 1.0 C06 A:XSY1202 4.6 18.2 1.0 CZ A:ARG1155 4.6 21.1 0.7 CG A:HIS1057 4.7 10.1 1.0 CB A:ARG1155 4.7 14.0 0.3 H061 A:XSY1202 4.7 21.8 1.0 HB3 A:ARG1155 4.7 16.8 0.3 CA A:ARG1155 4.8 11.1 0.7 CA A:ARG1155 4.8 11.1 0.3 HA A:ARG1155 4.8 13.4 0.3 C04 A:XSY1202 4.8 13.5 1.0 HB3 A:HIS1057 4.8 12.7 1.0 NE A:ARG1155 4.8 16.4 0.7 HA A:ARG1155 4.8 13.3 0.7 N10 A:XSY1202 4.8 10.1 1.0 NE2 A:HIS1057 4.9 9.8 1.0 C27 A:XSY1202 4.9 19.0 1.0 HD3 A:ARG1155 4.9 18.6 0.7 HB3 A:ARG1155 4.9 16.7 0.7 CB A:ASP1081 4.9 8.8 1.0 HB3 A:ASP1081 4.9 10.6 1.0 C08 A:XSY1202 4.9 11.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49


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 Hcv NS3/4A D168A Protease in Complex with NR04-49 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:25.4 occ:1.00 F55 A:XSY1202 0.0 25.4 1.0 C32 A:XSY1202 1.4 17.3 1.0 HH11 A:ARG1155 1.7 25.2 0.7 F54 A:XSY1202 2.2 23.0 1.0 F56 A:XSY1202 2.3 23.4 1.0 C25 A:XSY1202 2.3 14.8 1.0 HD2 A:ARG1155 2.5 18.6 0.7 NH1 A:ARG1155 2.5 21.0 0.7 N30 A:XSY1202 2.6 23.3 1.0 HD3 A:ARG1155 2.6 21.3 0.3 HD2 A:ARG1155 2.7 21.3 0.3 HH12 A:ARG1155 2.9 25.2 0.7 CD A:ARG1155 3.0 17.7 0.3 HG2 A:ARG1155 3.1 19.9 0.7 O A:HOH1360 3.1 46.1 1.0 HB2 A:ASP1081 3.2 10.6 1.0 CD A:ARG1155 3.3 15.5 0.7 HG2 A:ARG1155 3.3 22.9 0.3 HG3 A:ARG1155 3.4 19.9 0.7 CG A:ARG1155 3.5 16.6 0.7 OD2 A:ASP1081 3.5 12.4 1.0 CZ A:ARG1155 3.6 21.1 0.7 O A:HOH1450 3.7 35.8 1.0 CG A:ARG1155 3.7 19.1 0.3 C24 A:XSY1202 3.8 16.6 1.0 NE A:ARG1155 3.8 16.4 0.7 CB A:ASP1081 3.9 8.8 1.0 CG A:ASP1081 3.9 11.2 1.0 HB3 A:ASP1081 4.0 10.6 1.0 HB2 A:ALA1156 4.0 13.0 1.0 HD3 A:ARG1155 4.0 18.6 0.7 C28 A:XSY1202 4.1 25.6 1.0 HG3 A:ARG1155 4.2 22.9 0.3 O07 A:XSY1202 4.2 16.2 1.0 NE A:ARG1155 4.3 19.4 0.3 HH21 A:ARG1155 4.4 19.6 0.3 HD1 A:HIS1057 4.4 12.5 1.0 H492 A:XSY1202 4.6 26.5 1.0 HE A:ARG1155 4.7 19.7 0.7 NH2 A:ARG1155 4.7 27.2 0.7 HE A:ARG1155 4.8 23.2 0.3 H311 A:XSY1202 4.8 37.2 1.0 OD1 A:ASP1081 4.9 9.8 1.0 CB A:ALA1156 4.9 10.8 1.0 CB A:ARG1155 4.9 13.9 0.7 HH22 A:ARG1155 4.9 32.6 0.7 N26 A:XSY1202 4.9 23.7 1.0 HB3 A:ALA1156 5.0 13.0 1.0 NH2 A:ARG1155 5.0 16.3 0.3

Fluorine binding site 3 out of 3 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR04-49


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 Hcv NS3/4A D168A Protease in Complex with NR04-49 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:23.4 occ:1.00 F56 A:XSY1202 0.0 23.4 1.0 C32 A:XSY1202 1.4 17.3 1.0 F54 A:XSY1202 2.2 23.0 1.0 F55 A:XSY1202 2.3 25.4 1.0 C25 A:XSY1202 2.4 14.8 1.0 HH11 A:ARG1155 2.8 25.2 0.7 O07 A:XSY1202 2.8 16.2 1.0 HH12 A:ARG1155 2.9 25.2 0.7 C24 A:XSY1202 3.0 16.6 1.0 H492 A:XSY1202 3.1 26.5 1.0 O A:HOH1351 3.1 31.8 1.0 NH1 A:ARG1155 3.2 21.0 0.7 HB2 A:ALA1156 3.2 13.0 1.0 N30 A:XSY1202 3.5 23.3 1.0 HD2 A:ARG1155 3.8 21.3 0.3 O21 A:XSY1202 3.8 16.6 1.0 O A:HOH1462 3.8 40.0 1.0 C49 A:XSY1202 3.9 22.1 1.0 CB A:ALA1156 4.0 10.8 1.0 HB1 A:ALA1156 4.0 13.0 1.0 HG2 A:ARG1155 4.0 19.9 0.7 H491 A:XSY1202 4.1 26.5 1.0 H061 A:XSY1202 4.2 21.8 1.0 HB3 A:ALA1156 4.2 13.0 1.0 C05 A:XSY1202 4.3 14.7 1.0 H011 A:XSY1202 4.3 15.1 1.0 H481 A:XSY1202 4.3 20.1 1.0 N26 A:XSY1202 4.4 23.7 1.0 CZ A:ARG1155 4.5 21.1 0.7 HD2 A:ARG1155 4.5 18.6 0.7 HD3 A:ARG1155 4.5 21.3 0.3 CD A:ARG1155 4.5 17.7 0.3 N03 A:XSY1202 4.6 11.9 1.0 C06 A:XSY1202 4.6 18.2 1.0 C19 A:XSY1202 4.6 14.7 1.0 O A:HOH1360 4.7 46.1 1.0 C48 A:XSY1202 4.7 16.8 1.0 HG2 A:ARG1155 4.7 22.9 0.3 C28 A:XSY1202 4.7 25.6 1.0 C01 A:XSY1202 4.7 12.6 1.0 CG A:ARG1155 4.8 16.6 0.7 H051 A:XSY1202 4.8 17.6 1.0 HG3 A:ARG1155 4.9 19.9 0.7 CD A:ARG1155 5.0 15.5 0.7

D.Nageswara Rao, J.Zephyr, M.Henes, E.T.Chan, A.N.Matthew, A.K.Hedger, H.L.Conway, M.Saeed, A.Newton, C.J.Petropoulos, W.Huang, N.Kurt Yilmaz, C.A.Schiffer, A.Ali. Discovery of Quinoxaline-Based P1-P3 Macrocyclic NS3/4A Protease Inhibitors with Potent Activity Against Drug-Resistant Hepatitis C Virus Variants. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34405680
DOI: 10.1021/ACS.JMEDCHEM.1C00554