Fluorine in PDB 6vdl: Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir

All present enzymatic activity of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir:
2.7.7.48; 3.4.21.98; 3.6.1.15; 3.6.4.13;

The structure of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir, PDB code: 6vdl was solved by J.Timm, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.56 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.793, 58.601, 59.89, 90, 90, 90
R / Rfree (%)	15.2 / 20

The structure of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Fluorine atom in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir (pdb code 6vdl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir, PDB code: 6vdl:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:14.4 occ:1.00 F15 A:O311202 0.0 14.4 1.0 C14 A:O311202 1.4 13.9 1.0 H141 A:O311202 1.9 16.8 1.0 F16 A:O311202 2.2 15.5 1.0 C13 A:O311202 2.4 13.7 1.0 HA A:LYS1136 2.7 15.1 1.0 H131 A:O311202 2.8 16.5 1.0 O A:HOH1433 3.1 13.6 1.0 HD11 A:ILE1132 3.1 32.8 1.0 HG12 A:ILE1132 3.2 23.7 1.0 C11 A:O311202 3.4 13.6 1.0 O10 A:O311202 3.4 12.6 1.0 C09 A:O311202 3.4 14.0 1.0 CA A:LYS1136 3.6 12.5 1.0 HG13 A:ILE1132 3.6 23.7 1.0 CG1 A:ILE1132 3.7 19.7 1.0 HB2 A:LYS1136 3.7 17.2 1.0 O19 A:O311202 3.8 18.2 1.0 CD1 A:ILE1132 3.8 27.2 1.0 C12 A:O311202 3.8 12.8 1.0 N A:LYS1136 3.8 11.9 1.0 H121 A:O311202 4.0 15.5 1.0 HG3 A:LYS1136 4.0 16.2 1.0 HD13 A:ILE1132 4.0 32.8 1.0 H562 A:O311202 4.1 23.2 1.0 CB A:LYS1136 4.1 14.3 1.0 O A:LEU1135 4.1 11.7 1.0 C A:LEU1135 4.1 14.5 1.0 HB2 A:LEU1135 4.1 17.4 1.0 H A:LYS1136 4.2 14.3 1.0 N08 A:O311202 4.3 10.7 1.0 H A:GLY1137 4.3 12.8 1.0 HB2 A:ALA1157 4.3 18.8 1.0 N17 A:O311202 4.4 12.1 1.0 HB3 A:ALA1157 4.4 18.8 1.0 C18 A:O311202 4.5 13.9 1.0 O A:ILE1132 4.5 14.2 1.0 H122 A:O311202 4.5 15.5 1.0 CG A:LYS1136 4.6 13.4 1.0 O06 A:O311202 4.6 11.5 1.0 HD12 A:ILE1132 4.6 32.8 1.0 H583 A:O311202 4.6 22.6 1.0 H081 A:O311202 4.7 12.9 1.0 HB3 A:LEU1135 4.7 17.4 1.0 C A:LYS1136 4.7 13.6 1.0 CB A:LEU1135 4.8 14.5 1.0 O26 A:O311202 4.8 14.1 1.0 N A:GLY1137 4.9 10.6 1.0 CB A:ALA1157 4.9 15.6 1.0 C56 A:O311202 4.9 19.3 1.0 H563 A:O311202 4.9 23.2 1.0

Fluorine binding site 2 out of 4 in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:15.5 occ:1.00 F16 A:O311202 0.0 15.5 1.0 C14 A:O311202 1.4 13.9 1.0 H141 A:O311202 2.0 16.8 1.0 F15 A:O311202 2.2 14.4 1.0 C13 A:O311202 2.3 13.7 1.0 HB2 A:ALA1157 2.6 18.8 1.0 H131 A:O311202 2.6 16.5 1.0 HB2 A:LEU1135 2.7 17.4 1.0 HZ A:PHE1154 3.0 17.0 1.0 HB3 A:LEU1135 3.0 17.4 1.0 HG13 A:ILE1132 3.1 23.7 1.0 C12 A:O311202 3.2 12.8 1.0 H121 A:O311202 3.2 15.5 1.0 CB A:LEU1135 3.3 14.5 1.0 HB3 A:ALA1157 3.3 18.8 1.0 CB A:ALA1157 3.4 15.6 1.0 HD11 A:ILE1132 3.6 32.8 1.0 HG12 A:ILE1132 3.6 23.7 1.0 CZ A:PHE1154 3.7 14.1 1.0 C11 A:O311202 3.7 13.6 1.0 O A:LEU1135 3.7 11.7 1.0 H122 A:O311202 3.7 15.5 1.0 CG1 A:ILE1132 3.8 19.7 1.0 C A:LEU1135 3.8 14.5 1.0 HD12 A:LEU1135 3.8 18.0 1.0 HA A:LYS1136 3.9 15.1 1.0 HB1 A:ALA1157 3.9 18.8 1.0 HE2 A:PHE1154 4.0 18.0 1.0 O10 A:O311202 4.1 12.6 1.0 HD13 A:LEU1135 4.1 18.0 1.0 N A:LYS1136 4.1 11.9 1.0 CA A:LEU1135 4.2 14.7 1.0 CD1 A:ILE1132 4.2 27.2 1.0 CE2 A:PHE1154 4.2 15.0 1.0 C09 A:O311202 4.2 14.0 1.0 H A:ALA1157 4.2 20.0 1.0 CD1 A:LEU1135 4.3 15.0 1.0 H562 A:O311202 4.3 23.2 1.0 N A:ALA1157 4.4 16.6 1.0 CG A:LEU1135 4.4 15.2 1.0 CA A:ALA1157 4.4 17.4 1.0 H A:LYS1136 4.5 14.3 1.0 O A:ILE1132 4.5 14.2 1.0 CA A:LYS1136 4.5 12.5 1.0 CE1 A:PHE1154 4.7 10.7 1.0 HE1 A:PHE1154 4.7 12.9 1.0 HD12 A:ILE1132 4.7 32.8 1.0 HA A:ALA1157 4.7 20.9 1.0 HA A:ILE1132 4.8 16.0 1.0 H A:LEU1135 4.8 15.9 1.0 N17 A:O311202 4.8 12.1 1.0 HG A:LEU1135 4.9 18.3 1.0 HA A:LEU1135 4.9 17.7 1.0 HD13 A:ILE1132 4.9 32.8 1.0 O26 A:O311202 4.9 14.1 1.0 C A:THR1156 5.0 12.7 1.0

Fluorine binding site 3 out of 4 in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:26.1 occ:1.00 F53 A:O311202 0.0 26.1 1.0 C41 A:O311202 1.4 24.1 1.0 F54 A:O311202 2.2 23.0 1.0 H391 A:O311202 2.3 25.8 1.0 C42 A:O311202 2.3 15.6 1.0 C40 A:O311202 2.4 19.9 1.0 N43 A:O311202 2.7 20.6 1.0 C39 A:O311202 2.7 21.5 1.0 O A:HOH1386 2.8 29.9 1.0 O A:HOH1442 3.0 30.5 1.0 HB2 A:ASP1081 3.0 13.0 1.0 HD2 A:ARG1155 3.1 20.0 1.0 H401 A:O311202 3.2 24.0 1.0 C51 A:O311202 3.7 14.1 1.0 CB A:ASP1081 3.8 10.8 1.0 HG21 A:THR1156 4.0 27.3 1.0 HG2 A:ARG1155 4.0 20.4 1.0 HB3 A:ASP1081 4.0 13.0 1.0 OD2 A:ASP1081 4.0 13.8 1.0 CD A:ARG1155 4.0 16.6 1.0 O A:HOH1494 4.1 39.3 1.0 CG A:ASP1081 4.1 16.7 1.0 C44 A:O311202 4.2 23.8 1.0 C38 A:O311202 4.2 22.9 1.0 HG22 A:THR1156 4.3 27.3 1.0 O52 A:O311202 4.3 18.3 1.0 HG3 A:ARG1155 4.3 20.4 1.0 CG A:ARG1155 4.4 17.0 1.0 O A:HOH1483 4.4 36.2 1.0 CG2 A:THR1156 4.5 22.7 1.0 HG23 A:THR1156 4.6 27.3 1.0 H382 A:O311202 4.6 27.5 1.0 H381 A:O311202 4.7 27.5 1.0 HD3 A:ARG1155 4.7 20.0 1.0 NE A:ARG1155 4.7 20.6 1.0 H361 A:O311202 4.8 36.1 1.0 H451 A:O311202 4.8 25.2 1.0 N50 A:O311202 4.9 15.9 1.0 O37 A:O311202 4.9 29.3 1.0 HE A:ARG1155 5.0 24.8 1.0

Fluorine binding site 4 out of 4 in the Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS3/4A Protease A156T Mutant in Complex with Glecaprevir within 5.0Å range: probe atom residue distance (Å) B Occ A:F1202 b:23.0 occ:1.00 F54 A:O311202 0.0 23.0 1.0 C41 A:O311202 1.4 24.1 1.0 F53 A:O311202 2.2 26.1 1.0 C40 A:O311202 2.4 19.9 1.0 C42 A:O311202 2.4 15.6 1.0 HG23 A:THR1156 2.5 27.3 1.0 HG21 A:THR1156 2.6 27.3 1.0 HG22 A:THR1156 2.6 27.3 1.0 HG2 A:ARG1155 2.7 20.4 1.0 CG2 A:THR1156 2.7 22.7 1.0 H401 A:O311202 2.8 24.0 1.0 O52 A:O311202 3.0 18.3 1.0 C51 A:O311202 3.0 14.1 1.0 HG3 A:ARG1155 3.1 20.4 1.0 OD2 A:ASP1081 3.2 13.8 1.0 C39 A:O311202 3.3 21.5 1.0 CG A:ARG1155 3.3 17.0 1.0 HD2 A:ARG1155 3.3 20.0 1.0 H391 A:O311202 3.4 25.8 1.0 N43 A:O311202 3.5 20.6 1.0 H201 A:O311202 3.5 20.6 1.0 HB2 A:ASP1081 3.8 13.0 1.0 CD A:ARG1155 3.8 16.6 1.0 CG A:ASP1081 3.9 16.7 1.0 HD1 A:HIS1057 4.0 11.7 1.0 O A:ARG1155 4.1 13.2 1.0 HB3 A:ASP1081 4.2 13.0 1.0 CB A:ASP1081 4.2 10.8 1.0 CB A:THR1156 4.2 23.9 1.0 H361 A:O311202 4.3 36.1 1.0 C22 A:O311202 4.3 16.3 1.0 C20 A:O311202 4.3 17.1 1.0 N50 A:O311202 4.4 15.9 1.0 C A:ARG1155 4.5 11.8 1.0 ND1 A:HIS1057 4.5 9.7 1.0 HD3 A:ARG1155 4.5 20.0 1.0 H211 A:O311202 4.6 15.9 1.0 C38 A:O311202 4.6 22.9 1.0 CB A:ARG1155 4.6 16.9 1.0 N24 A:O311202 4.7 14.7 1.0 HB A:THR1156 4.7 28.8 1.0 H381 A:O311202 4.7 27.5 1.0 NE A:ARG1155 4.7 20.6 1.0 C21 A:O311202 4.7 13.2 1.0 HE A:ARG1155 4.7 24.8 1.0 C44 A:O311202 4.7 23.8 1.0 HE1 A:HIS1057 4.8 18.5 1.0 O A:HOH1442 4.8 30.5 1.0 H221 A:O311202 4.8 19.6 1.0 O A:HOH1386 4.9 29.9 1.0 OG1 A:THR1156 4.9 20.9 1.0 CE1 A:HIS1057 4.9 15.3 1.0 HA A:THR1156 4.9 18.1 1.0 N A:THR1156 4.9 13.7 1.0 OD1 A:ASP1081 4.9 13.3 1.0 H232 A:O311202 4.9 25.6 1.0 CA A:THR1156 5.0 15.0 1.0 HB3 A:ARG1155 5.0 20.3 1.0 C23 A:O311202 5.0 21.3 1.0

J.Timm, J.Zephyr, S.Hou, N.Kurt Yilmaz, C.A.Schiffer. Ras at Position 156 of Hcv NS3/4A Protease Abolish Inhibition By Current Hcv Drugs To Be Published.