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Fluorine in PDB 6p6m: Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir

Enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir

All present enzymatic activity of Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir:
3.4.21.98; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir, PDB code: 6p6m 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) 26.83 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.226, 58.550, 60.356, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 25.6

Other elements in 6p6m:

The structure of Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS3/4A Protease Domain of Genotype 1A C159 in Complex with Glecaprevir (pdb code 6p6m). 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 Domain of Genotype 1A C159 in Complex with Glecaprevir, PDB code: 6p6m:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6p6m

Go back to Fluorine Binding Sites List in 6p6m
Fluorine binding site 1 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A C159 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 Domain of Genotype 1A C159 in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:21.9
occ:1.00
F15 A:O311301 0.0 21.9 1.0
C14 A:O311301 1.4 18.8 1.0
H141 A:O311301 1.9 22.6 1.0
F16 A:O311301 2.2 21.2 1.0
C13 A:O311301 2.4 19.6 1.0
HB2 A:LEU1135 2.5 24.0 1.0
H131 A:O311301 2.6 23.5 1.0
HD11 A:ILE1132 2.7 37.2 1.0
HB2 A:ALA1157 2.7 27.3 1.0
HZ A:PHE1154 2.8 22.5 1.0
HB3 A:LEU1135 3.0 24.0 1.0
CB A:LEU1135 3.2 20.0 1.0
HD12 A:ILE1132 3.2 37.2 1.0
C12 A:O311301 3.3 17.8 1.0
HB3 A:ALA1157 3.3 27.3 1.0
H122 A:O311301 3.4 21.4 1.0
CD1 A:ILE1132 3.4 31.0 1.0
CB A:ALA1157 3.4 22.7 1.0
CZ A:PHE1154 3.5 18.8 1.0
HD12 A:LEU1135 3.6 25.5 1.0
HG13 A:ILE1132 3.7 39.0 1.0
HE2 A:PHE1154 3.7 22.9 1.0
C11 A:O311301 3.8 18.9 1.0
C A:LEU1135 3.8 22.0 1.0
O A:LEU1135 3.8 20.9 1.0
H121 A:O311301 3.9 21.4 1.0
HB1 A:ALA1157 3.9 27.3 1.0
HD13 A:LEU1135 4.0 25.5 1.0
CE2 A:PHE1154 4.0 19.0 1.0
HA A:LYS1136 4.1 28.5 1.0
O10 A:O311301 4.1 19.3 1.0
CD1 A:LEU1135 4.1 21.2 1.0
CG1 A:ILE1132 4.1 32.5 1.0
CA A:LEU1135 4.1 22.0 1.0
HD13 A:ILE1132 4.1 37.2 1.0
N A:LYS1136 4.2 20.1 1.0
CG A:LEU1135 4.2 22.7 1.0
C09 A:O311301 4.3 19.2 1.0
O A:ILE1132 4.4 28.8 1.0
H571 A:O311301 4.4 29.9 1.0
H A:LYS1136 4.5 24.1 1.0
CE1 A:PHE1154 4.5 17.1 1.0
HG12 A:ILE1132 4.6 39.0 1.0
N A:ALA1157 4.6 18.0 1.0
CA A:ALA1157 4.6 23.3 1.0
H A:ALA1157 4.6 21.7 1.0
HE1 A:PHE1154 4.6 20.5 1.0
CA A:LYS1136 4.6 23.7 1.0
HG A:LEU1135 4.7 27.3 1.0
H A:LEU1135 4.7 25.9 1.0
HA A:ILE1132 4.8 35.0 1.0
HA A:LEU1135 4.8 26.4 1.0
N17 A:O311301 4.9 18.0 1.0
H573 A:O311301 4.9 29.9 1.0
HA A:ALA1156 4.9 21.0 1.0
HA A:ALA1157 5.0 28.0 1.0
N A:LEU1135 5.0 21.6 1.0

Fluorine binding site 2 out of 4 in 6p6m

Go back to Fluorine Binding Sites List in 6p6m
Fluorine binding site 2 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A C159 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 Domain of Genotype 1A C159 in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:21.2
occ:1.00
F16 A:O311301 0.0 21.2 1.0
C14 A:O311301 1.4 18.8 1.0
H141 A:O311301 1.9 22.6 1.0
F15 A:O311301 2.2 21.9 1.0
C13 A:O311301 2.4 19.6 1.0
HA A:LYS1136 2.7 28.5 1.0
H131 A:O311301 2.8 23.5 1.0
O10 A:O311301 3.0 19.3 1.0
O A:HOH1481 3.2 30.8 1.0
C11 A:O311301 3.2 18.9 1.0
C09 A:O311301 3.2 19.2 1.0
HD11 A:ILE1132 3.3 37.2 1.0
HG13 A:ILE1132 3.4 39.0 1.0
CA A:LYS1136 3.5 23.7 1.0
O19 A:O311301 3.6 19.8 1.0
C12 A:O311301 3.7 17.8 1.0
N A:LYS1136 3.7 20.1 1.0
HB2 A:LYS1136 3.8 30.4 1.0
H122 A:O311301 3.8 21.4 1.0
HB2 A:LEU1135 3.9 24.0 1.0
C A:LEU1135 4.0 22.0 1.0
O A:LEU1135 4.0 20.9 1.0
HG3 A:LYS1136 4.0 33.5 1.0
H571 A:O311301 4.0 29.9 1.0
CD1 A:ILE1132 4.0 31.0 1.0
CG1 A:ILE1132 4.1 32.5 1.0
H A:LYS1136 4.1 24.1 1.0
CB A:LYS1136 4.1 25.3 1.0
HG12 A:ILE1132 4.2 39.0 1.0
N17 A:O311301 4.2 18.0 1.0
H A:GLY1137 4.2 26.5 1.0
N08 A:O311301 4.3 17.4 1.0
HD12 A:ILE1132 4.3 37.2 1.0
O A:ILE1132 4.3 28.8 1.0
C18 A:O311301 4.3 19.7 1.0
H121 A:O311301 4.5 21.4 1.0
H561 A:O311301 4.5 32.2 1.0
HB2 A:ALA1157 4.5 27.3 1.0
HB3 A:ALA1157 4.6 27.3 1.0
HB3 A:LEU1135 4.6 24.0 1.0
CG A:LYS1136 4.6 27.9 1.0
CB A:LEU1135 4.6 20.0 1.0
O07 A:O311301 4.7 25.1 1.0
C A:LYS1136 4.7 21.7 1.0
H081 A:O311301 4.7 21.0 1.0
N A:GLY1137 4.8 22.0 1.0
HZ A:PHE1154 4.8 22.5 1.0
HD13 A:ILE1132 4.8 37.2 1.0
O26 A:O311301 4.9 19.8 1.0
C57 A:O311301 4.9 24.9 1.0
CA A:LEU1135 4.9 22.0 1.0
H171 A:O311301 5.0 21.6 1.0

Fluorine binding site 3 out of 4 in 6p6m

Go back to Fluorine Binding Sites List in 6p6m
Fluorine binding site 3 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A C159 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 Domain of Genotype 1A C159 in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:20.3
occ:1.00
F53 A:O311301 0.0 20.3 1.0
C41 A:O311301 1.4 20.9 1.0
F54 A:O311301 2.2 22.4 1.0
H391 A:O311301 2.3 26.2 1.0
C42 A:O311301 2.4 19.6 1.0
C40 A:O311301 2.4 18.7 1.0
HD2 A:ARG1155 2.5 22.7 1.0
C39 A:O311301 2.7 21.8 1.0
N43 A:O311301 2.7 18.2 1.0
O A:HOH1440 2.9 24.5 1.0
HB2 A:ASP1081 3.0 19.6 1.0
H401 A:O311301 3.2 22.5 1.0
HG2 A:ARG1155 3.3 20.8 1.0
CD A:ARG1155 3.4 18.9 1.0
HG3 A:ARG1155 3.4 20.8 1.0
OD2 A:ASP1081 3.5 17.8 1.0
CG A:ARG1155 3.6 17.3 1.0
CB A:ASP1081 3.6 16.3 1.0
HB3 A:ASP1081 3.6 19.6 1.0
O A:HOH1445 3.7 24.2 1.0
C51 A:O311301 3.8 18.2 1.0
CG A:ASP1081 3.8 18.0 1.0
HD3 A:ARG1155 4.0 22.7 1.0
HB2 A:ALA1156 4.1 23.9 1.0
NE A:ARG1155 4.2 19.5 1.0
C44 A:O311301 4.2 21.2 1.0
C38 A:O311301 4.3 20.6 1.0
O52 A:O311301 4.3 21.3 1.0
O A:HOH1507 4.3 28.0 1.0
HE A:ARG1155 4.4 23.4 1.0
H361 A:O311301 4.4 25.5 1.0
O A:HOH1487 4.6 29.8 1.0
H382 A:O311301 4.6 24.7 1.0
H381 A:O311301 4.7 24.7 1.0
HD1 A:HIS1057 4.7 20.4 1.0
HB3 A:ALA1156 4.8 23.9 1.0
HH11 A:ARG1155 4.8 22.9 1.0
CB A:ALA1156 4.9 19.9 1.0
OD1 A:ASP1081 4.9 15.5 1.0
H451 A:O311301 4.9 22.2 1.0
N50 A:O311301 4.9 18.2 1.0
O37 A:O311301 4.9 24.2 1.0
CA A:ASP1081 5.0 15.8 1.0

Fluorine binding site 4 out of 4 in 6p6m

Go back to Fluorine Binding Sites List in 6p6m
Fluorine binding site 4 out of 4 in the Hcv NS3/4A Protease Domain of Genotype 1A C159 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 Domain of Genotype 1A C159 in Complex with Glecaprevir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1301

b:22.4
occ:1.00
F54 A:O311301 0.0 22.4 1.0
C41 A:O311301 1.4 20.9 1.0
F53 A:O311301 2.2 20.3 1.0
C42 A:O311301 2.4 19.6 1.0
HB2 A:ALA1156 2.4 23.9 1.0
C40 A:O311301 2.4 18.7 1.0
H401 A:O311301 2.8 22.5 1.0
O52 A:O311301 2.8 21.3 1.0
H201 A:O311301 2.9 23.8 1.0
C51 A:O311301 2.9 18.2 1.0
HG2 A:ARG1155 3.0 20.8 1.0
HG3 A:ARG1155 3.1 20.8 1.0
CB A:ALA1156 3.3 19.9 1.0
C39 A:O311301 3.4 21.8 1.0
OD2 A:ASP1081 3.4 17.8 1.0
CG A:ARG1155 3.5 17.3 1.0
N43 A:O311301 3.5 18.2 1.0
H391 A:O311301 3.5 26.2 1.0
O A:ARG1155 3.6 16.5 1.0
HB3 A:ALA1156 3.6 23.9 1.0
HB1 A:ALA1156 3.7 23.9 1.0
C20 A:O311301 3.7 19.8 1.0
HD2 A:ARG1155 3.8 22.7 1.0
HD1 A:HIS1057 4.0 20.4 1.0
H361 A:O311301 4.0 25.5 1.0
C22 A:O311301 4.0 19.0 1.0
C A:ARG1155 4.1 17.3 1.0
N24 A:O311301 4.1 17.9 1.0
H211 A:O311301 4.1 21.2 1.0
CD A:ARG1155 4.2 18.9 1.0
HE1 A:HIS1057 4.2 21.8 1.0
C21 A:O311301 4.3 17.6 1.0
CA A:ALA1156 4.3 17.5 1.0
H171 A:O311301 4.3 21.6 1.0
N50 A:O311301 4.3 18.2 1.0
HA A:ALA1156 4.3 21.0 1.0
CG A:ASP1081 4.3 18.0 1.0
ND1 A:HIS1057 4.3 17.0 1.0
N A:ALA1156 4.4 15.2 1.0
HB2 A:ASP1081 4.5 19.6 1.0
CE1 A:HIS1057 4.5 18.1 1.0
C23 A:O311301 4.7 17.1 1.0
HB3 A:ASP1081 4.7 19.6 1.0
H221 A:O311301 4.7 22.9 1.0
C38 A:O311301 4.7 20.6 1.0
C25 A:O311301 4.7 20.5 1.0
CB A:ARG1155 4.7 17.6 1.0
H381 A:O311301 4.8 24.7 1.0
CB A:ASP1081 4.8 16.3 1.0
H232 A:O311301 4.8 20.5 1.0
C44 A:O311301 4.8 21.2 1.0
O26 A:O311301 4.8 19.8 1.0
C18 A:O311301 4.8 19.7 1.0
N17 A:O311301 4.9 18.0 1.0
HD3 A:ARG1155 4.9 22.7 1.0
O30 A:O311301 4.9 22.5 1.0
C36 A:O311301 4.9 21.2 1.0
O A:HOH1440 5.0 24.5 1.0
CA A:ARG1155 5.0 17.3 1.0

Reference:

J.Timm, K.Kosovrasti, M.Henes, F.Leidner, S.Hou, N.Kurt-Yilmaz, C.A.Schiffer. Hcv NS3/4A Protease Domain of Genotype 1A in Complex with Glecaprevir To Be Published.
Page generated: Fri Aug 2 00:06:35 2024

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