Fluorine in PDB 7l7n: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59, PDB code: 7l7n 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)	24.05 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.623, 58.728, 60.209, 90, 90, 90
R / Rfree (%)	18.2 / 20.9

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59 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 NR02-59 (pdb code 7l7n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59, PDB code: 7l7n:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


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 NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:36.0 occ:1.00 F52 A:XSV1202 0.0 36.0 1.0 C32 A:XSV1202 1.4 32.6 1.0 HH11 A:ARG1155 2.0 41.3 1.0 F54 A:XSV1202 2.2 36.2 1.0 F53 A:XSV1202 2.2 36.9 1.0 C25 A:XSV1202 2.4 30.5 1.0 HD2 A:ARG1155 2.4 27.6 1.0 N30 A:XSV1202 2.7 33.2 1.0 NH1 A:ARG1155 2.8 34.4 1.0 HG2 A:ARG1155 3.1 30.2 1.0 HH12 A:ARG1155 3.2 41.3 1.0 CD A:ARG1155 3.2 23.0 1.0 HB2 A:ASP1081 3.3 19.1 1.0 HG3 A:ARG1155 3.4 30.2 1.0 CG A:ARG1155 3.4 25.1 1.0 OD1 A:ASP1081 3.5 16.4 1.0 O A:HOH1457 3.6 40.6 1.0 CZ A:ARG1155 3.7 41.1 1.0 C24 A:XSV1202 3.8 30.4 1.0 NE A:ARG1155 3.8 28.8 1.0 CB A:ASP1081 3.9 15.9 1.0 HD3 A:ARG1155 4.0 27.6 1.0 CG A:ASP1081 4.0 16.2 1.0 HB3 A:ASP1081 4.0 19.1 1.0 HB2 A:ALA1156 4.2 22.4 1.0 C28 A:XSV1202 4.2 32.3 1.0 O07 A:XSV1202 4.3 26.8 1.0 HD1 A:HIS1057 4.5 19.5 1.0 F56 A:XSV1202 4.5 39.0 1.0 HE A:ARG1155 4.6 34.5 1.0 NH2 A:ARG1155 4.8 44.8 1.0 CB A:ARG1155 4.9 18.9 1.0 N26 A:XSV1202 5.0 33.5 1.0 H011 A:XSV1202 5.0 29.8 1.0 OD2 A:ASP1081 5.0 16.4 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


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 NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:36.9 occ:1.00 F53 A:XSV1202 0.0 36.9 1.0 C32 A:XSV1202 1.4 32.6 1.0 F54 A:XSV1202 2.2 36.2 1.0 F52 A:XSV1202 2.2 36.0 1.0 C25 A:XSV1202 2.4 30.5 1.0 HH11 A:ARG1155 2.7 41.3 1.0 O07 A:XSV1202 2.9 26.8 1.0 F56 A:XSV1202 2.9 39.0 1.0 C24 A:XSV1202 3.0 30.4 1.0 HH12 A:ARG1155 3.1 41.3 1.0 NH1 A:ARG1155 3.2 34.4 1.0 HB2 A:ALA1156 3.4 22.4 1.0 N30 A:XSV1202 3.5 33.2 1.0 O21 A:XSV1202 3.8 24.5 1.0 HG2 A:ARG1155 4.0 30.2 1.0 CB A:ALA1156 4.1 18.7 1.0 H011 A:XSV1202 4.2 29.8 1.0 HB1 A:ALA1156 4.2 22.4 1.0 HB3 A:ALA1156 4.3 22.4 1.0 C51 A:XSV1202 4.3 46.1 1.0 C05 A:XSV1202 4.3 25.1 1.0 HD2 A:ARG1155 4.3 27.6 1.0 H061 A:XSV1202 4.4 31.6 1.0 N26 A:XSV1202 4.4 33.5 1.0 CZ A:ARG1155 4.5 41.1 1.0 C19 A:XSV1202 4.6 34.7 1.0 N03 A:XSV1202 4.6 22.8 1.0 H501 A:XSV1202 4.7 44.6 1.0 C06 A:XSV1202 4.7 26.4 1.0 CG A:ARG1155 4.7 25.1 1.0 C28 A:XSV1202 4.7 32.3 1.0 C01 A:XSV1202 4.8 24.8 1.0 HG3 A:ARG1155 4.8 30.2 1.0 H051 A:XSV1202 4.8 30.1 1.0 F57 A:XSV1202 4.9 43.4 1.0 CD A:ARG1155 4.9 23.0 1.0 F55 A:XSV1202 5.0 39.3 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


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 NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:36.2 occ:1.00 F54 A:XSV1202 0.0 36.2 1.0 C32 A:XSV1202 1.4 32.6 1.0 F52 A:XSV1202 2.2 36.0 1.0 F53 A:XSV1202 2.2 36.9 1.0 C25 A:XSV1202 2.4 30.5 1.0 HB2 A:ALA1156 2.6 22.4 1.0 HG2 A:ARG1155 2.6 30.2 1.0 HH11 A:ARG1155 2.7 41.3 1.0 H011 A:XSV1202 2.8 29.8 1.0 HG3 A:ARG1155 3.0 30.2 1.0 O07 A:XSV1202 3.0 26.8 1.0 C24 A:XSV1202 3.0 30.4 1.0 CG A:ARG1155 3.2 25.1 1.0 OD1 A:ASP1081 3.4 16.4 1.0 O A:ARG1155 3.4 16.5 1.0 N30 A:XSV1202 3.5 33.2 1.0 NH1 A:ARG1155 3.5 34.4 1.0 HD2 A:ARG1155 3.5 27.6 1.0 CB A:ALA1156 3.5 18.7 1.0 HD1 A:HIS1057 3.6 19.5 1.0 C01 A:XSV1202 3.7 24.8 1.0 HH12 A:ARG1155 3.8 41.3 1.0 HB3 A:ALA1156 3.9 22.4 1.0 ND1 A:HIS1057 3.9 16.2 1.0 CD A:ARG1155 3.9 23.0 1.0 HE1 A:HIS1057 3.9 22.7 1.0 C A:ARG1155 3.9 15.2 1.0 HB1 A:ALA1156 4.0 22.4 1.0 CE1 A:HIS1057 4.1 18.9 1.0 H101 A:XSV1202 4.2 20.3 1.0 N03 A:XSV1202 4.2 22.8 1.0 C05 A:XSV1202 4.2 25.1 1.0 H022 A:XSV1202 4.2 27.0 1.0 HA A:ALA1156 4.3 20.2 1.0 CA A:ALA1156 4.3 16.9 1.0 C02 A:XSV1202 4.3 22.5 1.0 F56 A:XSV1202 4.4 39.0 1.0 N26 A:XSV1202 4.4 33.5 1.0 N A:ALA1156 4.4 16.1 1.0 CG A:ASP1081 4.4 16.2 1.0 CB A:ARG1155 4.5 18.9 1.0 CZ A:ARG1155 4.5 41.1 1.0 NE A:ARG1155 4.7 28.8 1.0 C28 A:XSV1202 4.7 32.3 1.0 HD3 A:ARG1155 4.7 27.6 1.0 CA A:ARG1155 4.7 17.3 1.0 HB2 A:ASP1081 4.8 19.1 1.0 N10 A:XSV1202 4.8 16.9 1.0 C06 A:XSV1202 4.8 26.4 1.0 C04 A:XSV1202 4.8 22.3 1.0 HA A:ARG1155 4.8 20.7 1.0 H051 A:XSV1202 4.8 30.1 1.0 HB3 A:ARG1155 4.8 22.7 1.0 CG A:HIS1057 4.8 15.6 1.0 H061 A:XSV1202 4.9 31.6 1.0 C08 A:XSV1202 4.9 24.0 1.0 HB3 A:HIS1057 4.9 18.4 1.0 O21 A:XSV1202 5.0 24.5 1.0 HB3 A:ASP1081 5.0 19.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


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 Hcv NS3/4A D168A Protease in Complex with NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:39.3 occ:1.00 F55 A:XSV1202 0.0 39.3 1.0 C51 A:XSV1202 1.4 46.1 1.0 F57 A:XSV1202 2.2 43.4 1.0 F56 A:XSV1202 2.3 39.0 1.0 C48 A:XSV1202 2.3 43.8 1.0 O20 A:XSV1202 2.7 26.2 1.0 H492 A:XSV1202 2.7 53.9 1.0 HB3 A:ALA1156 2.9 22.4 1.0 C49 A:XSV1202 2.9 44.9 1.0 HG22 A:VAL1158 3.3 33.7 1.0 HB1 A:ALA1156 3.4 22.4 1.0 H491 A:XSV1202 3.4 53.9 1.0 HH12 A:ARG1155 3.4 41.3 1.0 CB A:ALA1156 3.5 18.7 1.0 CB A:ALA1168 3.6 17.9 1.0 C19 A:XSV1202 3.7 34.7 1.0 C50 A:XSV1202 3.7 37.1 1.0 NH2 A:ARG1123 3.8 51.3 1.0 HH21 A:ARG1123 3.8 61.5 1.0 H501 A:XSV1202 3.9 44.6 1.0 HH22 A:ARG1123 3.9 61.5 1.0 HH22 A:ARG1155 3.9 53.8 1.0 HB2 A:ALA1156 4.0 22.4 1.0 C60 A:XSV1202 4.0 49.1 1.0 NH1 A:ARG1155 4.1 34.4 1.0 O21 A:XSV1202 4.1 24.5 1.0 CG2 A:VAL1158 4.1 28.1 1.0 CZ A:ARG1123 4.2 46.5 1.0 HG23 A:VAL1158 4.3 33.7 1.0 H601 A:XSV1202 4.3 58.9 1.0 H502 A:XSV1202 4.3 44.6 1.0 HG21 A:VAL1158 4.4 33.7 1.0 NH2 A:ARG1155 4.5 44.8 1.0 HE A:ARG1123 4.5 45.6 1.0 HH11 A:ARG1155 4.5 41.3 1.0 NE A:ARG1123 4.5 38.0 1.0 N17 A:XSV1202 4.6 21.2 1.0 CZ A:ARG1155 4.7 41.1 1.0 NH1 A:ARG1123 4.7 45.0 1.0 H A:ALA1168 4.7 20.4 1.0 H171 A:XSV1202 4.7 25.5 1.0 C A:ALA1156 4.7 19.7 1.0 CA A:ALA1156 4.7 16.9 1.0 HH12 A:ARG1123 4.8 54.0 1.0 HA A:VAL1158 4.8 28.0 1.0 O A:ALA1157 4.8 23.6 1.0 O A:ALA1156 4.8 18.2 1.0 H602 A:XSV1202 4.9 58.9 1.0 CA A:ALA1168 4.9 15.3 1.0 F53 A:XSV1202 5.0 36.9 1.0 C A:ALA1157 5.0 22.1 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:39.0 occ:1.00 F56 A:XSV1202 0.0 39.0 1.0 C51 A:XSV1202 1.4 46.1 1.0 F57 A:XSV1202 2.2 43.4 1.0 F55 A:XSV1202 2.3 39.3 1.0 C48 A:XSV1202 2.3 43.8 1.0 HH12 A:ARG1155 2.6 41.3 1.0 H501 A:XSV1202 2.7 44.6 1.0 O21 A:XSV1202 2.8 24.5 1.0 O20 A:XSV1202 2.9 26.2 1.0 F53 A:XSV1202 2.9 36.9 1.0 C50 A:XSV1202 3.0 37.1 1.0 C19 A:XSV1202 3.1 34.7 1.0 HB3 A:ALA1156 3.2 22.4 1.0 NH1 A:ARG1155 3.3 34.4 1.0 HB1 A:ALA1156 3.3 22.4 1.0 HB2 A:ALA1156 3.5 22.4 1.0 HH11 A:ARG1155 3.5 41.3 1.0 CB A:ALA1156 3.5 18.7 1.0 H502 A:XSV1202 3.5 44.6 1.0 C49 A:XSV1202 3.7 44.9 1.0 H492 A:XSV1202 3.8 53.9 1.0 C60 A:XSV1202 4.0 49.1 1.0 C32 A:XSV1202 4.1 32.6 1.0 HH22 A:ARG1155 4.2 53.8 1.0 H601 A:XSV1202 4.2 58.9 1.0 H491 A:XSV1202 4.3 53.9 1.0 F54 A:XSV1202 4.4 36.2 1.0 N17 A:XSV1202 4.4 21.2 1.0 CZ A:ARG1155 4.4 41.1 1.0 F52 A:XSV1202 4.5 36.0 1.0 NH2 A:ARG1155 4.7 44.8 1.0 H171 A:XSV1202 4.8 25.5 1.0 H602 A:XSV1202 4.9 58.9 1.0 HG2 A:ARG1155 4.9 30.2 1.0 HH21 A:ARG1123 4.9 61.5 1.0 O07 A:XSV1202 5.0 26.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR02-59 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:43.4 occ:1.00 F57 A:XSV1202 0.0 43.4 1.0 C51 A:XSV1202 1.4 46.1 1.0 F56 A:XSV1202 2.2 39.0 1.0 F55 A:XSV1202 2.2 39.3 1.0 C48 A:XSV1202 2.3 43.8 1.0 H492 A:XSV1202 2.4 53.9 1.0 H501 A:XSV1202 2.6 44.6 1.0 C49 A:XSV1202 2.7 44.9 1.0 H601 A:XSV1202 2.8 58.9 1.0 C50 A:XSV1202 2.9 37.1 1.0 HH22 A:ARG1123 3.0 61.5 1.0 C60 A:XSV1202 3.1 49.1 1.0 HH21 A:ARG1123 3.1 61.5 1.0 NH2 A:ARG1123 3.2 51.3 1.0 HH12 A:ARG1155 3.4 41.3 1.0 O20 A:XSV1202 3.6 26.2 1.0 H491 A:XSV1202 3.7 53.9 1.0 HH22 A:ARG1155 3.8 53.8 1.0 H502 A:XSV1202 3.8 44.6 1.0 H602 A:XSV1202 4.0 58.9 1.0 CZ A:ARG1123 4.2 46.5 1.0 NH1 A:ARG1155 4.2 34.4 1.0 O21 A:XSV1202 4.4 24.5 1.0 C19 A:XSV1202 4.5 34.7 1.0 NH2 A:ARG1155 4.6 44.8 1.0 O A:HOH1329 4.6 42.8 1.0 HB3 A:ALA1156 4.6 22.4 1.0 HH12 A:ARG1123 4.7 54.0 1.0 HH11 A:ARG1155 4.8 41.3 1.0 HG22 A:VAL1158 4.8 33.7 1.0 HE A:ARG1123 4.8 45.6 1.0 NH1 A:ARG1123 4.8 45.0 1.0 F53 A:XSV1202 4.9 36.9 1.0 CZ A:ARG1155 4.9 41.1 1.0 NE A:ARG1123 4.9 38.0 1.0

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