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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6vdl:

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

Zinc (Zn) 1 atom

Fluorine Binding Sites:

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 6vdl

Go back to Fluorine Binding Sites List in 6vdl
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 6vdl

Go back to Fluorine Binding Sites List in 6vdl
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 6vdl

Go back to Fluorine Binding Sites List in 6vdl
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 6vdl

Go back to Fluorine Binding Sites List in 6vdl
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

Reference:

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.
Page generated: Sun Jan 24 15:54:55 2021

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