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Fluorine in PDB 6vdm: Hcv NS3/4A Protease A156T, D168E Double Mutant in Complex with Glecaprevir

Enzymatic activity of Hcv NS3/4A Protease A156T, D168E Double Mutant in Complex with Glecaprevir

All present enzymatic activity of Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir, PDB code: 6vdm 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) 23.71 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.337, 58.643, 60.056, 90, 90, 90
R / Rfree (%) 16.2 / 19.6

Other elements in 6vdm:

The structure of Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir (pdb code 6vdm). 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, D168E Double Mutant in Complex with Glecaprevir, PDB code: 6vdm:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6vdm

Go back to Fluorine Binding Sites List in 6vdm
Fluorine binding site 1 out of 4 in the Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:12.4
occ:1.00
F15 A:O311202 0.0 12.4 1.0
C14 A:O311202 1.4 11.2 1.0
F16 A:O311202 2.2 13.4 1.0
C13 A:O311202 2.4 12.1 1.0
HA A:LYS1136 2.6 10.8 1.0
HD11 A:ILE1132 3.0 30.5 1.0
O A:HOH1406 3.3 12.2 1.0
C11 A:O311202 3.3 11.2 1.0
O10 A:O311202 3.3 8.9 1.0
C09 A:O311202 3.4 9.7 1.0
HG13 A:ILE1132 3.4 26.6 1.0
CA A:LYS1136 3.4 9.0 1.0
HD12 A:ILE1132 3.4 30.5 1.0
CD1 A:ILE1132 3.5 25.4 1.0
HB2 A:LYS1136 3.5 12.9 1.0
N A:LYS1136 3.7 10.4 1.0
O19 A:O311202 3.7 11.6 1.0
C12 A:O311202 3.7 11.6 1.0
CG1 A:ILE1132 3.9 22.2 1.0
CB A:LYS1136 4.0 10.8 1.0
C A:LEU1135 4.0 11.6 1.0
H A:LYS1136 4.0 12.4 1.0
HB2 A:LEU1135 4.0 12.8 1.0
HG12 A:ILE1132 4.0 26.6 1.0
O A:LEU1135 4.1 10.9 1.0
HG3 A:LYS1136 4.1 15.6 1.0
N17 A:O311202 4.2 11.4 1.0
H A:GLY1137 4.2 10.1 1.0
N08 A:O311202 4.3 10.4 1.0
HB3 A:ALA1157 4.4 14.4 1.0
C18 A:O311202 4.4 12.1 1.0
HB2 A:ALA1157 4.4 14.4 1.0
HD13 A:ILE1132 4.4 30.5 1.0
O A:ILE1132 4.4 13.5 1.0
HB3 A:LEU1135 4.5 12.8 1.0
O07 A:O311202 4.5 9.8 1.0
CG A:LYS1136 4.6 13.0 1.0
C A:LYS1136 4.6 7.8 1.0
CB A:LEU1135 4.6 10.7 1.0
C56 A:O311202 4.7 13.3 1.0
N A:GLY1137 4.7 8.4 1.0
HB3 A:LYS1136 4.8 12.9 1.0
O26 A:O311202 4.8 14.6 1.0
CB A:ALA1157 4.9 12.0 1.0
CA A:LEU1135 4.9 11.2 1.0
HZ A:PHE1154 5.0 13.2 1.0
C58 A:O311202 5.0 12.4 1.0

Fluorine binding site 2 out of 4 in 6vdm

Go back to Fluorine Binding Sites List in 6vdm
Fluorine binding site 2 out of 4 in the Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:13.4
occ:1.00
F16 A:O311202 0.0 13.4 1.0
C14 A:O311202 1.4 11.2 1.0
F15 A:O311202 2.2 12.4 1.0
C13 A:O311202 2.3 12.1 1.0
HD11 A:ILE1132 2.5 30.5 1.0
HD12 A:ILE1132 2.5 30.5 1.0
HB2 A:ALA1157 2.6 14.4 1.0
HB2 A:LEU1135 2.7 12.8 1.0
CD1 A:ILE1132 2.9 25.4 1.0
HB3 A:LEU1135 2.9 12.8 1.0
HZ A:PHE1154 3.0 13.2 1.0
HB3 A:ALA1157 3.2 14.4 1.0
CB A:LEU1135 3.2 10.7 1.0
CB A:ALA1157 3.3 12.0 1.0
C12 A:O311202 3.3 11.6 1.0
HD13 A:ILE1132 3.6 30.5 1.0
HD12 A:LEU1135 3.7 15.2 1.0
CZ A:PHE1154 3.7 11.0 1.0
C11 A:O311202 3.8 11.2 1.0
C A:LEU1135 3.8 11.6 1.0
HB1 A:ALA1157 3.8 14.4 1.0
O A:LEU1135 3.9 10.9 1.0
HG13 A:ILE1132 3.9 26.6 1.0
HA A:LYS1136 3.9 10.8 1.0
CG1 A:ILE1132 4.0 22.2 1.0
HE2 A:PHE1154 4.1 13.0 1.0
N A:LYS1136 4.1 10.4 1.0
HD13 A:LEU1135 4.1 15.2 1.0
CA A:LEU1135 4.1 11.2 1.0
O10 A:O311202 4.2 8.9 1.0
CD1 A:LEU1135 4.2 12.7 1.0
H A:ALA1157 4.3 15.2 1.0
CE2 A:PHE1154 4.3 10.8 1.0
CG A:LEU1135 4.3 11.7 1.0
C09 A:O311202 4.3 9.7 1.0
H A:LYS1136 4.4 12.4 1.0
HG12 A:ILE1132 4.4 26.6 1.0
N A:ALA1157 4.4 12.7 1.0
CA A:ALA1157 4.4 13.7 1.0
CA A:LYS1136 4.5 9.0 1.0
O A:ILE1132 4.5 13.5 1.0
CE1 A:PHE1154 4.7 11.2 1.0
HE1 A:PHE1154 4.7 13.4 1.0
HG A:LEU1135 4.7 14.1 1.0
HA A:ILE1132 4.7 18.6 1.0
N17 A:O311202 4.8 11.4 1.0
H A:LEU1135 4.8 14.1 1.0
HA A:ALA1157 4.8 16.4 1.0
C56 A:O311202 4.8 13.3 1.0
HA A:LEU1135 4.8 13.4 1.0
O26 A:O311202 4.9 14.6 1.0
HB2 A:LYS1136 5.0 12.9 1.0

Fluorine binding site 3 out of 4 in 6vdm

Go back to Fluorine Binding Sites List in 6vdm
Fluorine binding site 3 out of 4 in the Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:38.0
occ:1.00
F53 A:O311202 0.0 38.0 1.0
C41 A:O311202 1.4 32.2 1.0
F54 A:O311202 2.2 35.2 1.0
C42 A:O311202 2.4 24.1 1.0
C40 A:O311202 2.4 31.8 1.0
N43 A:O311202 2.8 22.0 1.0
C39 A:O311202 2.8 34.4 1.0
O A:HOH1459 3.3 33.6 1.0
HB2 A:ASP1081 3.4 12.5 1.0
OG1 A:THR1156 3.5 18.4 1.0
O A:HOH1453 3.6 39.7 1.0
CD A:ARG1155 3.6 17.0 0.6
O A:HOH1301 3.7 24.6 1.0
C51 A:O311202 3.7 21.0 1.0
O A:HOH1423 3.7 49.8 1.0
OD2 A:ASP1081 3.9 11.8 1.0
CB A:ASP1081 4.1 10.4 1.0
CD A:ARG1155 4.2 17.2 0.4
O52 A:O311202 4.2 20.1 1.0
NH2 A:ARG1155 4.2 20.3 0.6
HB3 A:ASP1081 4.2 12.5 1.0
CG A:ASP1081 4.3 12.1 1.0
C44 A:O311202 4.3 22.6 1.0
C38 A:O311202 4.4 35.5 1.0
NE A:ARG1155 4.4 19.5 0.4
NE A:ARG1155 4.4 18.5 0.6
CG A:ARG1155 4.6 15.8 0.4
CG A:ARG1155 4.6 15.7 0.6
CZ A:ARG1155 4.7 20.6 0.6
CB A:THR1156 4.7 15.2 1.0
CG2 A:THR1156 4.8 19.3 1.0
N50 A:O311202 4.9 20.6 1.0

Fluorine binding site 4 out of 4 in 6vdm

Go back to Fluorine Binding Sites List in 6vdm
Fluorine binding site 4 out of 4 in the Hcv NS3/4A Protease A156T, D168E Double 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, D168E Double Mutant in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:35.2
occ:1.00
F54 A:O311202 0.0 35.2 1.0
C41 A:O311202 1.4 32.2 1.0
F53 A:O311202 2.2 38.0 1.0
C42 A:O311202 2.4 24.1 1.0
C40 A:O311202 2.4 31.8 1.0
O52 A:O311202 2.7 20.1 1.0
OG1 A:THR1156 2.7 18.4 1.0
C51 A:O311202 2.9 21.0 1.0
C39 A:O311202 3.3 34.4 1.0
C20 A:O311202 3.5 13.0 1.0
N43 A:O311202 3.5 22.0 1.0
O A:ARG1155 3.6 9.7 1.0
CG2 A:THR1156 3.6 19.3 1.0
CB A:THR1156 3.7 15.2 1.0
OD2 A:ASP1081 3.7 11.8 1.0
C22 A:O311202 3.9 16.8 1.0
C21 A:O311202 3.9 13.7 1.0
N24 A:O311202 4.0 14.0 1.0
C A:ARG1155 4.2 10.7 1.0
CA A:THR1156 4.2 12.6 1.0
N50 A:O311202 4.2 20.6 1.0
CD A:ARG1155 4.3 17.0 0.6
O A:HOH1301 4.4 24.6 1.0
ND1 A:HIS1057 4.5 9.8 1.0
C23 A:O311202 4.5 15.8 1.0
N A:THR1156 4.5 11.7 1.0
CG A:ARG1155 4.6 15.8 0.4
C25 A:O311202 4.6 14.8 1.0
CG A:ARG1155 4.6 15.7 0.6
CE1 A:HIS1057 4.6 10.7 1.0
CG A:ASP1081 4.6 12.1 1.0
C38 A:O311202 4.6 35.5 1.0
O26 A:O311202 4.7 14.6 1.0
CB A:ARG1155 4.7 13.8 0.6
HB2 A:ASP1081 4.7 12.5 1.0
CB A:ARG1155 4.7 13.8 0.4
C44 A:O311202 4.8 22.6 1.0
C18 A:O311202 4.8 12.1 1.0
CD A:ARG1155 4.9 17.2 0.4
N17 A:O311202 5.0 11.4 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: Fri Aug 2 03:00:04 2024

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