Fluorine in PDB 7l7l: Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129, PDB code: 7l7l 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)	20.99 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.856, 58.773, 59.98, 90, 90, 90
R / Rfree (%)	16.6 / 20.8

The structure of Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129 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 NR01- 129 (pdb code 7l7l). 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 NR01- 129, PDB code: 7l7l:
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 NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:35.8 occ:1.00 F52 A:XSS1205 0.0 35.8 1.0 C32 A:XSS1205 1.4 27.9 1.0 F54 A:XSS1205 2.2 34.2 1.0 F53 A:XSS1205 2.2 36.9 1.0 C25 A:XSS1205 2.4 27.7 1.0 O A:HOH1435 2.8 51.2 1.0 O07 A:XSS1205 2.8 24.5 1.0 H502 A:XSS1205 2.9 32.6 1.0 H503 A:XSS1205 2.9 32.6 1.0 C24 A:XSS1205 3.0 27.1 1.0 C50 A:XSS1205 3.3 27.2 1.0 HB2 A:ALA1156 3.4 27.2 1.0 O A:HOH1440 3.5 45.3 1.0 N30 A:XSS1205 3.5 33.7 1.0 H501 A:XSS1205 3.7 32.6 1.0 O21 A:XSS1205 3.8 23.8 1.0 HB3 A:ALA1156 3.9 27.2 1.0 O A:HOH1311 4.0 32.9 1.0 CB A:ALA1156 4.1 22.7 1.0 HG2 A:ARG1155 4.1 33.5 1.0 C05 A:XSS1205 4.3 24.6 1.0 H062 A:XSS1205 4.3 28.1 1.0 HD2 A:ARG1155 4.3 32.0 1.0 HB1 A:ALA1156 4.3 27.2 1.0 N26 A:XSS1205 4.4 34.1 1.0 H011 A:XSS1205 4.4 31.0 1.0 C19 A:XSS1205 4.5 25.3 1.0 C48 A:XSS1205 4.6 27.9 1.0 N03 A:XSS1205 4.7 19.6 1.0 C06 A:XSS1205 4.7 23.4 1.0 C28 A:XSS1205 4.7 29.5 1.0 H051 A:XSS1205 4.8 29.6 1.0 CG A:ARG1155 4.8 27.9 1.0 H493 A:XSS1205 4.8 35.6 1.0 C01 A:XSS1205 4.9 25.9 1.0 HG3 A:ARG1155 4.9 33.5 1.0 O20 A:XSS1205 4.9 26.3 1.0 CD A:ARG1155 5.0 26.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:36.9 occ:1.00 F53 A:XSS1205 0.0 36.9 1.0 C32 A:XSS1205 1.4 27.9 1.0 F54 A:XSS1205 2.2 34.2 1.0 F52 A:XSS1205 2.2 35.8 1.0 C25 A:XSS1205 2.3 27.7 1.0 HD2 A:ARG1155 2.4 32.0 1.0 N30 A:XSS1205 2.7 33.7 1.0 O A:HOH1440 2.9 45.3 1.0 HG2 A:ARG1155 3.2 33.5 1.0 CD A:ARG1155 3.3 26.7 1.0 HB2 A:ASP1081 3.3 25.7 1.0 HG3 A:ARG1155 3.5 33.5 1.0 CG A:ARG1155 3.5 27.9 1.0 OD2 A:ASP1081 3.6 20.2 1.0 O A:HOH1311 3.6 32.9 1.0 C24 A:XSS1205 3.7 27.1 1.0 CB A:ASP1081 3.9 21.4 1.0 HD3 A:ARG1155 3.9 32.0 1.0 NE A:ARG1155 4.0 26.4 1.0 HB3 A:ASP1081 4.0 25.7 1.0 CG A:ASP1081 4.0 23.3 1.0 C28 A:XSS1205 4.1 29.5 1.0 HE A:ARG1155 4.1 31.7 1.0 O07 A:XSS1205 4.2 24.5 1.0 O A:HOH1435 4.2 51.2 1.0 H503 A:XSS1205 4.4 32.6 1.0 HB2 A:ALA1156 4.5 27.2 1.0 HB3 A:ALA1156 4.5 27.2 1.0 HD1 A:HIS1057 4.7 23.5 1.0 H502 A:XSS1205 4.7 32.6 1.0 HH11 A:ARG1155 4.9 42.1 1.0 N26 A:XSS1205 4.9 34.1 1.0 CZ A:ARG1155 4.9 36.0 1.0 C50 A:XSS1205 4.9 27.2 1.0 CB A:ALA1156 4.9 22.7 1.0 H501 A:XSS1205 5.0 32.6 1.0 H311 A:XSS1205 5.0 43.9 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:34.2 occ:1.00 F54 A:XSS1205 0.0 34.2 1.0 C32 A:XSS1205 1.4 27.9 1.0 F52 A:XSS1205 2.2 35.8 1.0 F53 A:XSS1205 2.2 36.9 1.0 C25 A:XSS1205 2.3 27.7 1.0 HG2 A:ARG1155 2.7 33.5 1.0 HB2 A:ALA1156 2.8 27.2 1.0 O07 A:XSS1205 2.9 24.5 1.0 C24 A:XSS1205 3.0 27.1 1.0 H011 A:XSS1205 3.0 31.0 1.0 HG3 A:ARG1155 3.0 33.5 1.0 CG A:ARG1155 3.3 27.9 1.0 OD2 A:ASP1081 3.3 20.2 1.0 HB3 A:ALA1156 3.4 27.2 1.0 N30 A:XSS1205 3.4 33.7 1.0 CB A:ALA1156 3.5 22.7 1.0 O A:ARG1155 3.5 19.6 1.0 HD2 A:ARG1155 3.5 32.0 1.0 HD1 A:HIS1057 3.7 23.5 1.0 C01 A:XSS1205 3.8 25.9 1.0 HE1 A:HIS1057 3.9 25.7 1.0 CD A:ARG1155 4.0 26.7 1.0 C A:ARG1155 4.0 15.9 1.0 ND1 A:HIS1057 4.0 19.6 1.0 C05 A:XSS1205 4.1 24.6 1.0 H503 A:XSS1205 4.1 32.6 1.0 CE1 A:HIS1057 4.1 21.4 1.0 H021 A:XSS1205 4.1 24.9 1.0 HB1 A:ALA1156 4.2 27.2 1.0 N03 A:XSS1205 4.2 19.6 1.0 O A:HOH1311 4.3 32.9 1.0 N26 A:XSS1205 4.3 34.1 1.0 C02 A:XSS1205 4.3 20.8 1.0 HA A:ALA1156 4.3 22.5 1.0 CA A:ALA1156 4.3 18.8 1.0 CG A:ASP1081 4.4 23.3 1.0 H101 A:XSS1205 4.4 20.7 1.0 N A:ALA1156 4.4 18.3 1.0 CB A:ARG1155 4.5 20.5 1.0 O A:HOH1440 4.6 45.3 1.0 HB2 A:ASP1081 4.6 25.7 1.0 C28 A:XSS1205 4.6 29.5 1.0 H051 A:XSS1205 4.7 29.6 1.0 O A:HOH1435 4.7 51.2 1.0 HD3 A:ARG1155 4.7 32.0 1.0 HE A:ARG1155 4.7 31.7 1.0 CA A:ARG1155 4.7 20.7 1.0 C06 A:XSS1205 4.8 23.4 1.0 H502 A:XSS1205 4.8 32.6 1.0 NE A:ARG1155 4.8 26.4 1.0 H062 A:XSS1205 4.8 28.1 1.0 HA A:ARG1155 4.8 24.8 1.0 HB3 A:ARG1155 4.9 24.6 1.0 HB3 A:ASP1081 4.9 25.7 1.0 C50 A:XSS1205 4.9 27.2 1.0 C08 A:XSS1205 4.9 19.3 1.0 C04 A:XSS1205 4.9 22.5 1.0 CB A:ASP1081 4.9 21.4 1.0 CG A:HIS1057 4.9 19.8 1.0 N10 A:XSS1205 4.9 17.2 1.0 C27 A:XSS1205 5.0 27.3 1.0 HB3 A:HIS1057 5.0 25.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:30.9 occ:1.00 F55 A:XSS1205 0.0 30.9 1.0 C51 A:XSS1205 1.4 31.2 1.0 F56 A:XSS1205 2.2 29.9 1.0 F57 A:XSS1205 2.3 30.3 1.0 C48 A:XSS1205 2.4 27.9 1.0 O20 A:XSS1205 2.6 26.3 1.0 H503 A:XSS1205 2.8 32.6 1.0 H501 A:XSS1205 2.8 32.6 1.0 C50 A:XSS1205 2.8 27.2 1.0 HG22 A:VAL1158 2.9 34.0 1.0 HB1 A:ALA1156 3.2 27.2 1.0 C49 A:XSS1205 3.8 29.7 1.0 H502 A:XSS1205 3.8 32.6 1.0 HB3 A:ALA1156 3.8 27.2 1.0 CG2 A:VAL1158 3.8 28.3 1.0 CB A:ALA1168 3.9 17.7 1.0 C19 A:XSS1205 3.9 25.3 1.0 CB A:ALA1156 4.0 22.7 1.0 H492 A:XSS1205 4.0 35.6 1.0 H491 A:XSS1205 4.1 35.6 1.0 O A:HOH1456 4.1 39.3 1.0 HG23 A:VAL1158 4.1 34.0 1.0 HG21 A:VAL1158 4.2 34.0 1.0 HA A:VAL1158 4.2 27.2 1.0 O A:HOH1311 4.3 32.9 1.0 O A:ALA1157 4.3 23.7 1.0 H493 A:XSS1205 4.4 35.6 1.0 HB2 A:ALA1156 4.5 27.2 1.0 C A:ALA1157 4.6 25.3 1.0 H171 A:XSS1205 4.6 29.6 1.0 H A:ALA1168 4.7 24.1 1.0 O21 A:XSS1205 4.7 23.8 1.0 N17 A:XSS1205 4.7 24.6 1.0 C A:ALA1156 4.7 22.5 1.0 N A:VAL1158 4.7 23.7 1.0 O A:ALA1156 4.8 19.7 1.0 HG13 A:VAL1158 4.8 38.7 1.0 CA A:VAL1158 4.8 22.7 1.0 O A:HOH1374 4.9 32.0 1.0 CB A:VAL1158 4.9 23.0 1.0 CA A:ALA1156 5.0 18.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:29.9 occ:1.00 F56 A:XSS1205 0.0 29.9 1.0 C51 A:XSS1205 1.4 31.2 1.0 F55 A:XSS1205 2.2 30.9 1.0 F57 A:XSS1205 2.3 30.3 1.0 C48 A:XSS1205 2.3 27.9 1.0 O20 A:XSS1205 2.6 26.3 1.0 H491 A:XSS1205 2.8 35.6 1.0 HG22 A:VAL1158 2.9 34.0 1.0 C49 A:XSS1205 3.0 29.7 1.0 H492 A:XSS1205 3.1 35.6 1.0 HA A:VAL1158 3.2 27.2 1.0 O A:HOH1374 3.4 32.0 1.0 HG13 A:VAL1158 3.4 38.7 1.0 C50 A:XSS1205 3.7 27.2 1.0 CG2 A:VAL1158 3.7 28.3 1.0 H501 A:XSS1205 3.8 32.6 1.0 H493 A:XSS1205 3.9 35.6 1.0 C19 A:XSS1205 3.9 25.3 1.0 H503 A:XSS1205 4.0 32.6 1.0 CA A:VAL1158 4.0 22.7 1.0 HG21 A:VAL1158 4.0 34.0 1.0 O A:ALA1157 4.1 23.7 1.0 CG1 A:VAL1158 4.2 32.2 1.0 CB A:VAL1158 4.2 23.0 1.0 H171 A:XSS1205 4.3 29.6 1.0 H502 A:XSS1205 4.4 32.6 1.0 HG23 A:VAL1158 4.4 34.0 1.0 N17 A:XSS1205 4.6 24.6 1.0 N A:VAL1158 4.6 23.7 1.0 C A:ALA1157 4.6 25.3 1.0 HG12 A:VAL1158 4.6 38.7 1.0 HB1 A:ALA1156 4.7 27.2 1.0 H A:SER1159 4.7 33.8 1.0 O21 A:XSS1205 4.7 23.8 1.0 HG11 A:VAL1158 4.9 38.7 1.0 O A:HOH1456 5.0 39.3 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Hcv NS3/4A D168A Protease in Complex with NR01- 129


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 NR01- 129 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1205 b:30.3 occ:1.00 F57 A:XSS1205 0.0 30.3 1.0 C51 A:XSS1205 1.4 31.2 1.0 F56 A:XSS1205 2.3 29.9 1.0 F55 A:XSS1205 2.3 30.9 1.0 C48 A:XSS1205 2.4 27.9 1.0 H501 A:XSS1205 2.5 32.6 1.0 H492 A:XSS1205 2.6 35.6 1.0 C50 A:XSS1205 3.0 27.2 1.0 C49 A:XSS1205 3.0 29.7 1.0 H491 A:XSS1205 3.5 35.6 1.0 H503 A:XSS1205 3.6 32.6 1.0 O20 A:XSS1205 3.6 26.3 1.0 H502 A:XSS1205 3.7 32.6 1.0 H493 A:XSS1205 3.8 35.6 1.0 O A:HOH1456 4.2 39.3 1.0 HG22 A:VAL1158 4.2 34.0 1.0 C19 A:XSS1205 4.8 25.3 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