Fluorine in PDB 7mm6: Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49

Enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49

All present enzymatic activity of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49:
3.4.21.98;

Protein crystallography data

The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49, PDB code: 7mm6 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) 26.18 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.613, 58.646, 59.648, 90, 90, 90
R / Rfree (%) 17.4 / 19.6

Other elements in 7mm6:

The structure of Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49 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 NR02-49 (pdb code 7mm6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49, PDB code: 7mm6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7mm6

Go back to Fluorine Binding Sites List in 7mm6
Fluorine binding site 1 out of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49


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 NR02-49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:27.8
occ:1.00
F55 A:ZJY1202 0.0 27.8 1.0
C54 A:ZJY1202 1.4 23.6 1.0
F57 A:ZJY1202 2.2 28.2 1.0
F56 A:ZJY1202 2.2 22.0 1.0
C51 A:ZJY1202 2.4 28.3 1.0
H521 A:ZJY1202 2.4 37.4 1.0
HH21 A:ARG1123 2.5 41.6 1.0
H532 A:ZJY1202 2.6 32.0 1.0
HB2 A:ASP1168 2.7 17.9 1.0
HE A:ARG1123 2.7 36.7 1.0
NH2 A:ARG1123 2.7 34.6 1.0
C52 A:ZJY1202 2.8 31.0 1.0
C53 A:ZJY1202 2.9 26.5 1.0
NE A:ARG1123 3.0 30.4 1.0
CZ A:ARG1123 3.0 36.5 1.0
HH22 A:ARG1123 3.3 41.6 1.0
HG22 A:VAL1158 3.3 30.0 1.0
CB A:ASP1168 3.4 14.7 1.0
HB3 A:ASP1168 3.6 17.9 1.0
HG21 A:VAL1158 3.7 30.0 1.0
O A:HOH1429 3.7 33.6 1.0
H522 A:ZJY1202 3.7 37.4 1.0
O A:HOH1313 3.8 25.1 1.0
C17 A:ZJY1202 3.8 23.1 1.0
H531 A:ZJY1202 3.8 32.0 1.0
CG2 A:VAL1158 3.9 24.8 1.0
CG A:ASP1168 3.9 19.4 1.0
HG23 A:VAL1158 4.0 30.0 1.0
H171 A:ZJY1202 4.0 27.9 1.0
NH1 A:ARG1123 4.0 44.9 1.0
HD3 A:ARG1123 4.0 38.7 1.0
CD A:ARG1123 4.1 32.1 1.0
OD1 A:ASP1168 4.3 15.4 1.0
HD2 A:ARG1123 4.3 38.7 1.0
OD2 A:ASP1168 4.3 21.3 1.0
HH12 A:ARG1123 4.4 54.0 1.0
O15 A:ZJY1202 4.4 19.7 1.0
H172 A:ZJY1202 4.4 27.9 1.0
HH11 A:ARG1123 4.5 54.0 1.0
O A:HOH1345 4.6 24.1 1.0
HB3 A:ALA1156 4.7 16.8 1.0
CA A:ASP1168 4.7 14.8 1.0
HB1 A:ALA1156 4.7 16.8 1.0
HA A:ASP1168 4.8 18.0 1.0

Fluorine binding site 2 out of 3 in 7mm6

Go back to Fluorine Binding Sites List in 7mm6
Fluorine binding site 2 out of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49


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 NR02-49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:22.0
occ:1.00
F56 A:ZJY1202 0.0 22.0 1.0
C54 A:ZJY1202 1.4 23.6 1.0
F57 A:ZJY1202 2.2 28.2 1.0
F55 A:ZJY1202 2.2 27.8 1.0
C51 A:ZJY1202 2.4 28.3 1.0
HG22 A:VAL1158 2.6 30.0 1.0
HB1 A:ALA1156 2.7 16.8 1.0
HB3 A:ASP1168 2.8 17.9 1.0
HB2 A:ASP1168 3.0 17.9 1.0
H532 A:ZJY1202 3.0 32.0 1.0
O15 A:ZJY1202 3.1 19.7 1.0
C17 A:ZJY1202 3.1 23.1 1.0
C53 A:ZJY1202 3.1 26.5 1.0
H171 A:ZJY1202 3.2 27.9 1.0
HB3 A:ALA1156 3.2 16.8 1.0
CB A:ASP1168 3.3 14.7 1.0
CB A:ALA1156 3.4 13.9 1.0
CG2 A:VAL1158 3.4 24.8 1.0
HG23 A:VAL1158 3.4 30.0 1.0
C52 A:ZJY1202 3.7 31.0 1.0
H531 A:ZJY1202 3.7 32.0 1.0
HG21 A:VAL1158 3.8 30.0 1.0
C14 A:ZJY1202 3.8 17.9 1.0
H521 A:ZJY1202 3.9 37.4 1.0
O A:ALA1157 4.0 18.6 1.0
H172 A:ZJY1202 4.0 27.9 1.0
C A:ALA1156 4.0 14.5 1.0
C A:ALA1157 4.0 19.4 1.0
HB2 A:ALA1156 4.1 16.8 1.0
H131 A:ZJY1202 4.1 20.2 1.0
CG A:ASP1168 4.1 19.4 1.0
O A:ALA1156 4.2 15.9 1.0
N A:ALA1157 4.2 16.0 1.0
H A:ASP1168 4.2 18.6 1.0
OD2 A:ASP1168 4.2 21.3 1.0
N A:VAL1158 4.3 19.0 1.0
HA A:VAL1158 4.3 26.2 1.0
CA A:ALA1156 4.3 15.3 1.0
N13 A:ZJY1202 4.3 16.7 1.0
H A:ALA1157 4.4 19.4 1.0
H522 A:ZJY1202 4.5 37.4 1.0
N A:ASP1168 4.5 15.3 1.0
CA A:ASP1168 4.6 14.8 1.0
O16 A:ZJY1202 4.6 18.0 1.0
H A:VAL1158 4.6 23.0 1.0
CA A:VAL1158 4.6 21.7 1.0
CA A:ALA1157 4.6 16.3 1.0
CB A:VAL1158 4.6 23.8 1.0
HE A:ARG1123 4.6 36.7 1.0
HH21 A:ARG1123 4.7 41.6 1.0
HA A:ALA1157 4.7 19.7 1.0
NE A:ARG1123 4.8 30.4 1.0
NH2 A:ARG1123 4.8 34.6 1.0
CZ A:ARG1123 4.9 36.5 1.0

Fluorine binding site 3 out of 3 in 7mm6

Go back to Fluorine Binding Sites List in 7mm6
Fluorine binding site 3 out of 3 in the Crystal Structure of Hcv NS3/4A Protease in Complex with NR02-49


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 NR02-49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1202

b:28.2
occ:1.00
F57 A:ZJY1202 0.0 28.2 1.0
C54 A:ZJY1202 1.4 23.6 1.0
F55 A:ZJY1202 2.2 27.8 1.0
F56 A:ZJY1202 2.2 22.0 1.0
C51 A:ZJY1202 2.4 28.3 1.0
H171 A:ZJY1202 2.6 27.9 1.0
C17 A:ZJY1202 3.0 23.1 1.0
O A:HOH1345 3.0 24.1 1.0
HB3 A:ALA1156 3.1 16.8 1.0
OD2 A:ASP1168 3.1 21.3 1.0
HB3 A:ASP1168 3.2 17.9 1.0
HB2 A:ASP1168 3.2 17.9 1.0
C52 A:ZJY1202 3.3 31.0 1.0
CG A:ASP1168 3.4 19.4 1.0
H521 A:ZJY1202 3.4 37.4 1.0
HB1 A:ALA1156 3.4 16.8 1.0
CB A:ASP1168 3.5 14.7 1.0
CB A:ALA1156 3.7 13.9 1.0
H172 A:ZJY1202 3.7 27.9 1.0
C53 A:ZJY1202 3.7 26.5 1.0
H332 A:ZJY1202 3.8 21.0 1.0
O15 A:ZJY1202 3.8 19.7 1.0
H333 A:ZJY1202 3.9 21.0 1.0
H532 A:ZJY1202 4.0 32.0 1.0
H522 A:ZJY1202 4.0 37.4 1.0
O A:HOH1429 4.0 33.6 1.0
HB2 A:ALA1156 4.1 16.8 1.0
H331 A:ZJY1202 4.1 21.0 1.0
OD1 A:ASP1168 4.1 15.4 1.0
C33 A:ZJY1202 4.1 17.4 1.0
HH21 A:ARG1123 4.2 41.6 1.0
HE A:ARG1123 4.4 36.7 1.0
C14 A:ZJY1202 4.4 17.9 1.0
H531 A:ZJY1202 4.5 32.0 1.0
O16 A:ZJY1202 4.6 18.0 1.0
HG22 A:VAL1158 4.7 30.0 1.0
HE A:ARG1155 4.7 19.7 1.0
NH2 A:ARG1123 4.7 34.6 1.0
O A:HOH1313 4.8 25.1 1.0
NE A:ARG1123 5.0 30.4 1.0
CA A:ALA1156 5.0 15.3 1.0
HG2 A:ARG1155 5.0 17.7 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: Wed Apr 5 00:15:11 2023

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