Fluorine in PDB 7mm5: Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60

Enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60

All present enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60:
3.4.21.98;

Protein crystallography data

The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60, PDB code: 7mm5 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) 20.94 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.276, 58.629, 59.834, 90, 90, 90
R / Rfree (%) 18.2 / 20.6

Other elements in 7mm5:

The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60 (pdb code 7mm5). 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 Protease in Complex with NR02-60, PDB code: 7mm5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 1 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:27.4
occ:0.24
 F56 A:ZK41202 0.0 27.4 0.2
H542 A:ZK41202 1.3 33.2 0.8
H541 A:ZK41202 1.3 33.2 0.8
C55 A:ZK41202 1.4 26.2 0.2
C54 A:ZK41202 1.6 27.7 0.8
F57 A:ZK41202 2.2 30.3 0.2
F58 A:ZK41202 2.2 24.8 0.2
C17 A:ZK41202 2.4 25.2 0.2
C17 A:ZK41202 2.5 25.0 0.8
F58 A:ZK41202 2.8 27.1 0.8
O15 A:ZK41202 2.8 21.4 0.8
O15 A:ZK41202 2.8 21.3 0.2
H511 A:ZK41202 2.8 36.7 0.2
C51 A:ZK41202 2.9 30.6 0.2
C53 A:ZK41202 3.0 27.9 0.8
H512 A:ZK41202 3.0 36.7 0.2
C55 A:ZK41202 3.1 31.0 0.8
H532 A:ZK41202 3.2 33.5 0.8
H531 A:ZK41202 3.3 33.5 0.8
C14 A:ZK41202 3.4 23.6 0.2
C14 A:ZK41202 3.5 23.7 0.8
C54 A:ZK41202 3.6 24.8 0.2
F57 A:ZK41202 3.6 34.5 0.8
O16 A:ZK41202 3.7 19.9 0.2
H542 A:ZK41202 3.7 29.8 0.2
O16 A:ZK41202 3.8 19.5 0.8
C51 A:ZK41202 4.0 26.4 0.8
H541 A:ZK41202 4.1 29.8 0.2
C52 A:ZK41202 4.1 29.4 0.8
C52 A:ZK41202 4.2 29.5 0.2
F56 A:ZK41202 4.3 24.6 0.8
O A:HOH1389 4.3 34.9 1.0
H521 A:ZK41202 4.4 35.3 0.8
N13 A:ZK41202 4.5 17.6 0.2
H512 A:ZK41202 4.5 31.7 0.8
H521 A:ZK41202 4.5 35.4 0.2
H511 A:ZK41202 4.5 31.7 0.8
N13 A:ZK41202 4.6 17.0 0.8
H131 A:ZK41202 4.6 21.2 0.2
C53 A:ZK41202 4.6 25.4 0.2
H131 A:ZK41202 4.6 20.5 0.8
H522 A:ZK41202 4.8 35.4 0.2
H522 A:ZK41202 4.9 35.3 0.8

Fluorine binding site 2 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 2 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:24.6
occ:0.76
 F56 A:ZK41202 0.0 24.6 0.8
H521 A:ZK41202 0.5 35.4 0.2
C52 A:ZK41202 0.6 29.5 0.2
C55 A:ZK41202 1.4 31.0 0.8
H522 A:ZK41202 1.5 35.4 0.2
C51 A:ZK41202 1.7 30.6 0.2
C53 A:ZK41202 1.7 25.4 0.2
H532 A:ZK41202 2.0 30.5 0.2
H511 A:ZK41202 2.0 36.7 0.2
F58 A:ZK41202 2.2 27.1 0.8
F57 A:ZK41202 2.2 34.5 0.8
C17 A:ZK41202 2.3 25.0 0.8
H512 A:ZK41202 2.4 36.7 0.2
C17 A:ZK41202 2.4 25.2 0.2
H531 A:ZK41202 2.5 30.5 0.2
C54 A:ZK41202 2.6 24.8 0.2
H511 A:ZK41202 2.6 31.7 0.8
O15 A:ZK41202 2.7 21.3 0.2
O15 A:ZK41202 2.7 21.4 0.8
HG22 A:VAL1158 2.8 35.0 1.0
C51 A:ZK41202 2.9 26.4 0.8
HB2 A:ASP1168 3.0 18.4 1.0
H541 A:ZK41202 3.1 29.8 0.2
HB3 A:ASP1168 3.1 18.4 1.0
H512 A:ZK41202 3.2 31.7 0.8
HB3 A:ALA1156 3.3 16.4 1.0
H542 A:ZK41202 3.4 29.8 0.2
HG23 A:VAL1158 3.5 35.0 1.0
CB A:ASP1168 3.5 15.3 1.0
CG2 A:VAL1158 3.5 29.2 1.0
C54 A:ZK41202 3.5 27.7 0.8
HB1 A:ALA1156 3.6 16.4 1.0
H542 A:ZK41202 3.6 33.2 0.8
C55 A:ZK41202 3.8 26.2 0.2
C14 A:ZK41202 3.9 23.7 0.8
HG21 A:VAL1158 3.9 35.0 1.0
C14 A:ZK41202 3.9 23.6 0.2
CB A:ALA1156 3.9 13.7 1.0
NH2 A:ARG1123 4.0 42.8 1.0
HH21 A:ARG1123 4.0 51.4 1.0
CG A:ASP1168 4.1 26.6 1.0
C52 A:ZK41202 4.1 29.4 0.8
H541 A:ZK41202 4.2 33.2 0.8
CZ A:ARG1123 4.2 39.0 1.0
OD2 A:ASP1168 4.2 30.6 1.0
HH22 A:ARG1123 4.2 51.4 1.0
F56 A:ZK41202 4.3 27.4 0.2
F57 A:ZK41202 4.3 30.3 0.2
O A:ALA1157 4.4 18.4 1.0
C53 A:ZK41202 4.4 27.9 0.8
HE A:ARG1123 4.4 43.2 1.0
NE A:ARG1123 4.5 36.0 1.0
HA A:VAL1158 4.5 22.3 1.0
H522 A:ZK41202 4.6 35.3 0.8
O16 A:ZK41202 4.6 19.5 0.8
H531 A:ZK41202 4.6 33.5 0.8
H131 A:ZK41202 4.6 20.5 0.8
HB2 A:ALA1156 4.6 16.4 1.0
C A:ALA1157 4.6 21.6 1.0
O16 A:ZK41202 4.6 19.9 0.2
C A:ALA1156 4.7 15.0 1.0
N13 A:ZK41202 4.7 17.0 0.8
NH1 A:ARG1123 4.7 44.5 1.0
H131 A:ZK41202 4.7 21.2 0.2
H A:ASP1168 4.7 15.6 1.0
O A:ALA1156 4.7 14.6 1.0
CB A:VAL1158 4.8 21.8 1.0
H521 A:ZK41202 4.8 35.3 0.8
N13 A:ZK41202 4.8 17.6 0.2
N A:VAL1158 4.8 17.0 1.0
F58 A:ZK41202 4.8 24.8 0.2
CA A:ASP1168 4.8 15.2 1.0
HH12 A:ARG1123 4.9 53.4 1.0
CA A:VAL1158 4.9 18.6 1.0
N A:ALA1157 4.9 17.1 1.0
CA A:ALA1156 4.9 13.6 1.0
HG13 A:VAL1158 5.0 32.5 1.0
N A:ASP1168 5.0 13.0 1.0
OD1 A:ASP1168 5.0 24.7 1.0

Fluorine binding site 3 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 3 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:30.3
occ:0.24
 F57 A:ZK41202 0.0 30.3 0.2
H531 A:ZK41202 1.2 33.5 0.8
H542 A:ZK41202 1.2 33.2 0.8
C53 A:ZK41202 1.3 27.9 0.8
C55 A:ZK41202 1.4 26.2 0.2
C54 A:ZK41202 1.4 27.7 0.8
H532 A:ZK41202 1.8 33.5 0.8
H541 A:ZK41202 2.1 33.2 0.8
F56 A:ZK41202 2.2 27.4 0.2
F58 A:ZK41202 2.2 24.8 0.2
H542 A:ZK41202 2.3 29.8 0.2
C17 A:ZK41202 2.4 25.2 0.2
C17 A:ZK41202 2.5 25.0 0.8
H512 A:ZK41202 2.5 36.7 0.2
C52 A:ZK41202 2.8 29.4 0.8
F57 A:ZK41202 2.8 34.5 0.8
C54 A:ZK41202 2.8 24.8 0.2
C51 A:ZK41202 2.9 30.6 0.2
C55 A:ZK41202 3.1 31.0 0.8
C51 A:ZK41202 3.1 26.4 0.8
H522 A:ZK41202 3.2 35.3 0.8
H521 A:ZK41202 3.4 35.3 0.8
H511 A:ZK41202 3.5 31.7 0.8
H511 A:ZK41202 3.5 36.7 0.2
H541 A:ZK41202 3.5 29.8 0.2
F58 A:ZK41202 3.5 27.1 0.8
O15 A:ZK41202 3.6 21.4 0.8
O15 A:ZK41202 3.6 21.3 0.2
C53 A:ZK41202 3.8 25.4 0.2
H531 A:ZK41202 3.9 30.5 0.2
H512 A:ZK41202 4.0 31.7 0.8
C52 A:ZK41202 4.0 29.5 0.2
O16 A:ZK41202 4.1 19.9 0.2
O16 A:ZK41202 4.2 19.5 0.8
F56 A:ZK41202 4.3 24.6 0.8
C14 A:ZK41202 4.3 23.6 0.2
C14 A:ZK41202 4.3 23.7 0.8
H522 A:ZK41202 4.4 35.4 0.2
H521 A:ZK41202 4.7 35.4 0.2
H532 A:ZK41202 4.7 30.5 0.2
HH22 A:ARG1123 5.0 51.4 1.0

Fluorine binding site 4 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 4 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:34.5
occ:0.76
 F57 A:ZK41202 0.0 34.5 0.8
H512 A:ZK41202 0.7 36.7 0.2
C51 A:ZK41202 1.2 30.6 0.2
C55 A:ZK41202 1.4 31.0 0.8
C52 A:ZK41202 1.7 29.5 0.2
H522 A:ZK41202 1.7 35.4 0.2
H511 A:ZK41202 2.0 36.7 0.2
F56 A:ZK41202 2.2 24.6 0.8
F58 A:ZK41202 2.2 27.1 0.8
C53 A:ZK41202 2.3 25.4 0.2
H531 A:ZK41202 2.3 30.5 0.2
C17 A:ZK41202 2.4 25.0 0.8
C17 A:ZK41202 2.4 25.2 0.2
H542 A:ZK41202 2.5 33.2 0.8
H521 A:ZK41202 2.6 35.4 0.2
C54 A:ZK41202 2.7 24.8 0.2
H511 A:ZK41202 2.7 31.7 0.8
C54 A:ZK41202 2.8 27.7 0.8
F57 A:ZK41202 2.8 30.3 0.2
HH22 A:ARG1123 2.8 51.4 1.0
H542 A:ZK41202 2.8 29.8 0.2
HH21 A:ARG1123 2.8 51.4 1.0
NH2 A:ARG1123 2.9 42.8 1.0
C51 A:ZK41202 3.0 26.4 0.8
H531 A:ZK41202 3.0 33.5 0.8
C55 A:ZK41202 3.1 26.2 0.2
H532 A:ZK41202 3.2 30.5 0.2
C53 A:ZK41202 3.3 27.9 0.8
O15 A:ZK41202 3.5 21.3 0.2
O15 A:ZK41202 3.6 21.4 0.8
F56 A:ZK41202 3.6 27.4 0.2
H541 A:ZK41202 3.6 29.8 0.2
C52 A:ZK41202 3.7 29.4 0.8
H541 A:ZK41202 3.7 33.2 0.8
CZ A:ARG1123 3.8 39.0 1.0
H512 A:ZK41202 3.8 31.7 0.8
H522 A:ZK41202 3.9 35.3 0.8
HG22 A:VAL1158 4.0 35.0 1.0
H532 A:ZK41202 4.2 33.5 0.8
F58 A:ZK41202 4.3 24.8 0.2
HH12 A:ARG1123 4.3 53.4 1.0
HB2 A:ASP1168 4.3 18.4 1.0
HE A:ARG1123 4.3 43.2 1.0
NH1 A:ARG1123 4.4 44.5 1.0
NE A:ARG1123 4.4 36.0 1.0
H521 A:ZK41202 4.6 35.3 0.8
C14 A:ZK41202 4.8 23.7 0.8
C14 A:ZK41202 4.8 23.6 0.2
CG2 A:VAL1158 4.9 29.2 1.0
HB3 A:ASP1168 4.9 18.4 1.0
CB A:ASP1168 5.0 15.3 1.0
HG21 A:VAL1158 5.0 35.0 1.0

Fluorine binding site 5 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 5 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:24.8
occ:0.24
 F58 A:ZK41202 0.0 24.8 0.2
H541 A:ZK41202 1.0 33.2 0.8
C55 A:ZK41202 1.4 26.2 0.2
C54 A:ZK41202 1.6 27.7 0.8
H532 A:ZK41202 1.6 33.5 0.8
C53 A:ZK41202 1.8 27.9 0.8
F57 A:ZK41202 2.2 30.3 0.2
F56 A:ZK41202 2.2 27.4 0.2
O16 A:ZK41202 2.3 19.9 0.2
H542 A:ZK41202 2.3 33.2 0.8
C17 A:ZK41202 2.4 25.2 0.2
O16 A:ZK41202 2.4 19.5 0.8
C17 A:ZK41202 2.5 25.0 0.8
H521 A:ZK41202 2.6 35.3 0.8
C52 A:ZK41202 2.6 29.4 0.8
H531 A:ZK41202 2.7 33.5 0.8
H542 A:ZK41202 2.7 29.8 0.2
C14 A:ZK41202 2.8 23.6 0.2
C14 A:ZK41202 2.8 23.7 0.8
C54 A:ZK41202 2.9 24.8 0.2
O15 A:ZK41202 2.9 21.4 0.8
O15 A:ZK41202 2.9 21.3 0.2
H541 A:ZK41202 3.0 29.8 0.2
C51 A:ZK41202 3.1 26.4 0.8
H512 A:ZK41202 3.4 31.7 0.8
H522 A:ZK41202 3.5 35.3 0.8
C55 A:ZK41202 3.8 31.0 0.8
C51 A:ZK41202 3.9 30.6 0.2
H511 A:ZK41202 3.9 31.7 0.8
H512 A:ZK41202 4.0 36.7 0.2
N13 A:ZK41202 4.1 17.0 0.8
N13 A:ZK41202 4.1 17.6 0.2
H511 A:ZK41202 4.2 36.7 0.2
F58 A:ZK41202 4.2 27.1 0.8
F57 A:ZK41202 4.3 34.5 0.8
C53 A:ZK41202 4.4 25.4 0.2
H111 A:ZK41202 4.6 18.3 0.2
H111 A:ZK41202 4.6 18.2 0.8
H131 A:ZK41202 4.6 20.5 0.8
H131 A:ZK41202 4.6 21.2 0.2
H333 A:ZK41202 4.8 24.8 0.8
C52 A:ZK41202 4.8 29.5 0.2
F56 A:ZK41202 4.8 24.6 0.8
H531 A:ZK41202 4.8 30.5 0.2
H333 A:ZK41202 4.9 24.8 0.2
H041 A:ZK41202 4.9 21.3 0.8
C11 A:ZK41202 4.9 15.3 0.2
C11 A:ZK41202 4.9 15.2 0.8
H041 A:ZK41202 5.0 21.2 0.2
H532 A:ZK41202 5.0 30.5 0.2

Fluorine binding site 6 out of 6 in 7mm5

Go back to Fluorine Binding Sites List in 7mm5
Fluorine binding site 6 out of 6 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-60


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 Protease in Complex with NR02-60 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:27.1
occ:0.76
 F58 A:ZK41202 0.0 27.1 0.8
H511 A:ZK41202 0.2 36.7 0.2
C51 A:ZK41202 1.2 30.6 0.2
C55 A:ZK41202 1.4 31.0 0.8
H512 A:ZK41202 1.8 36.7 0.2
C52 A:ZK41202 2.1 29.5 0.2
F56 A:ZK41202 2.2 24.6 0.8
F57 A:ZK41202 2.2 34.5 0.8
H521 A:ZK41202 2.3 35.4 0.2
C17 A:ZK41202 2.3 25.2 0.2
C17 A:ZK41202 2.4 25.0 0.8
H542 A:ZK41202 2.5 33.2 0.8
HG22 A:VAL1158 2.6 35.0 1.0
O15 A:ZK41202 2.6 21.3 0.2
O15 A:ZK41202 2.6 21.4 0.8
H522 A:ZK41202 2.6 35.4 0.2
F56 A:ZK41202 2.8 27.4 0.2
C54 A:ZK41202 2.8 27.7 0.8
C55 A:ZK41202 3.0 26.2 0.2
H541 A:ZK41202 3.3 33.2 0.8
C53 A:ZK41202 3.4 25.4 0.2
C54 A:ZK41202 3.4 24.8 0.2
CG2 A:VAL1158 3.5 29.2 1.0
HG13 A:VAL1158 3.5 32.5 1.0
F57 A:ZK41202 3.5 30.3 0.2
HA A:VAL1158 3.7 22.3 1.0
C51 A:ZK41202 3.9 26.4 0.8
HH22 A:ARG1123 3.9 51.4 1.0
HG21 A:VAL1158 3.9 35.0 1.0
C14 A:ZK41202 3.9 23.6 0.2
H511 A:ZK41202 3.9 31.7 0.8
H542 A:ZK41202 4.0 29.8 0.2
H531 A:ZK41202 4.0 30.5 0.2
HG23 A:VAL1158 4.0 35.0 1.0
C14 A:ZK41202 4.0 23.7 0.8
H532 A:ZK41202 4.0 30.5 0.2
H541 A:ZK41202 4.0 29.8 0.2
NH2 A:ARG1123 4.2 42.8 1.0
O A:HOH1389 4.2 34.9 1.0
C53 A:ZK41202 4.2 27.9 0.8
F58 A:ZK41202 4.2 24.8 0.2
CB A:VAL1158 4.3 21.8 1.0
CG1 A:VAL1158 4.3 27.1 1.0
HH12 A:ARG1123 4.3 53.4 1.0
H531 A:ZK41202 4.3 33.5 0.8
H512 A:ZK41202 4.3 31.7 0.8
CA A:VAL1158 4.4 18.6 1.0
O A:ALA1157 4.5 18.4 1.0
HH21 A:ARG1123 4.5 51.4 1.0
CZ A:ARG1123 4.5 39.0 1.0
NH1 A:ARG1123 4.5 44.5 1.0
H131 A:ZK41202 4.5 20.5 0.8
H131 A:ZK41202 4.6 21.2 0.2
HG11 A:VAL1158 4.6 32.5 1.0
O16 A:ZK41202 4.7 19.9 0.2
C52 A:ZK41202 4.7 29.4 0.8
N13 A:ZK41202 4.8 17.6 0.2
O16 A:ZK41202 4.8 19.5 0.8
N13 A:ZK41202 4.8 17.0 0.8
N A:VAL1158 4.9 17.0 1.0
H532 A:ZK41202 4.9 33.5 0.8
HB2 A:ASP1168 4.9 18.4 1.0
C A:ALA1157 5.0 21.6 1.0

Reference:

J.Zephyr, D.Nageswara Rao, S.V.Vo, M.Henes, K.Kosovrasti, A.N.Matthew, A.K.Hedger, J.Timm, E.T.Chan, A.Ali, N.Kurt Yilmaz, C.A.Schiffer. Deciphering the Molecular Mechanism of Hcv Protease Inhibitor Fluorination As A General Approach to Avoid Drug Resistance. J.Mol.Biol. V. 434 67503 2022.
ISSN: ESSN 1089-8638
PubMed: 35183560
DOI: 10.1016/J.JMB.2022.167503
Page generated: Fri Aug 2 09:31:36 2024

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