Atomistry » Fluorine » PDB 9ars-9cdk » 9bpf
Atomistry »
  Fluorine »
    PDB 9ars-9cdk »
      9bpf »

Fluorine in PDB 9bpf: Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor

Enzymatic activity of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor

All present enzymatic activity of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor, PDB code: 9bpf was solved by P.Chen, E.Arutyunova, M.J.Lemieux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.33 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.489, 53.703, 114.802, 90, 101.08, 90
R / Rfree (%) 22.8 / 27.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor (pdb code 9bpf). 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 Main Protease of Sars-Cov-2 Complexed with Inhibitor, PDB code: 9bpf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 1 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.3
occ:1.00
 F1 A:YDL401 0.0 38.3 1.0
C21 A:YDL401 1.4 39.1 1.0
F3 A:YDL401 2.2 43.2 1.0
F2 A:YDL401 2.3 34.7 1.0
C11 A:YDL401 2.3 36.9 1.0
C12 A:YDL401 2.8 35.7 1.0
O A:ASP187 3.5 33.4 1.0
CB A:HIS41 3.6 32.5 1.0
OH A:TYR54 3.6 36.3 1.0
CG A:HIS41 3.7 35.4 1.0
C A:ASP187 3.7 33.2 1.0
CD2 A:HIS41 3.8 34.3 1.0
C10 A:YDL401 3.8 36.9 1.0
C8 A:YDL401 4.0 33.6 1.0
CB A:ASP187 4.0 29.7 1.0
CA A:ASP187 4.1 33.9 1.0
CG A:MET49 4.2 50.8 1.0
N A:ARG188 4.2 34.8 1.0
N3 A:YDL401 4.4 32.9 1.0
ND1 A:HIS41 4.4 35.5 1.0
CB A:MET49 4.5 48.9 1.0
NE2 A:HIS41 4.6 35.3 1.0
CA A:ARG188 4.6 38.3 1.0
SD A:MET49 4.9 63.6 1.0
CE1 A:HIS41 4.9 32.8 1.0
C A:ARG188 4.9 37.5 1.0
CE A:MET49 5.0 50.4 1.0

Fluorine binding site 2 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 2 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.7
occ:1.00
 F2 A:YDL401 0.0 34.7 1.0
C21 A:YDL401 1.4 39.1 1.0
F3 A:YDL401 2.2 43.2 1.0
F1 A:YDL401 2.3 38.3 1.0
C11 A:YDL401 2.4 36.9 1.0
C12 A:YDL401 2.8 35.7 1.0
C8 A:YDL401 3.0 33.6 1.0
N3 A:YDL401 3.1 32.9 1.0
C10 A:YDL401 3.1 36.9 1.0
CE A:MET165 3.5 36.0 1.0
CB A:MET165 3.7 30.9 1.0
C13 A:YDL401 4.0 35.2 1.0
SD A:MET165 4.0 37.3 1.0
CA A:ASP187 4.1 33.9 1.0
C A:ASP187 4.1 33.2 1.0
N A:ARG188 4.2 34.8 1.0
O A:HIS164 4.3 28.1 1.0
CB A:ASP187 4.3 29.7 1.0
C9 A:YDL401 4.4 35.3 1.0
O3 A:YDL401 4.4 32.3 1.0
CD2 A:HIS41 4.5 34.3 1.0
CG A:MET165 4.5 30.9 1.0
O A:ASP187 4.6 33.4 1.0
C A:ARG188 4.6 37.5 1.0
CA A:MET165 4.7 30.8 1.0
O A:ARG188 4.7 36.4 1.0
C14 A:YDL401 4.8 30.2 1.0
O4 A:YDL401 4.8 38.9 1.0
CA A:ARG188 4.8 38.3 1.0
NE2 A:HIS41 4.8 35.3 1.0
N A:GLN189 4.9 38.6 1.0
CG A:HIS41 4.9 35.4 1.0

Fluorine binding site 3 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 3 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:43.2
occ:1.00
 F3 A:YDL401 0.0 43.2 1.0
C21 A:YDL401 1.4 39.1 1.0
F2 A:YDL401 2.2 34.7 1.0
F1 A:YDL401 2.2 38.3 1.0
C11 A:YDL401 2.5 36.9 1.0
C10 A:YDL401 3.0 36.9 1.0
N A:GLN189 3.0 38.6 1.0
C A:ARG188 3.1 37.5 1.0
N A:ARG188 3.4 34.8 1.0
CA A:ARG188 3.4 38.3 1.0
C12 A:YDL401 3.6 35.7 1.0
O A:ARG188 3.6 36.4 1.0
C A:ASP187 3.7 33.2 1.0
CA A:GLN189 3.7 39.4 1.0
N3 A:YDL401 3.8 32.9 1.0
CB A:GLN189 3.8 38.0 1.0
O A:ASP187 3.9 33.4 1.0
CB A:MET49 4.1 48.9 1.0
O A:MET49 4.1 42.8 1.0
C8 A:YDL401 4.3 33.6 1.0
O4 A:YDL401 4.4 38.9 1.0
CE A:MET165 4.4 36.0 1.0
CA A:ASP187 4.4 33.9 1.0
CG A:MET49 4.5 50.8 1.0
C13 A:YDL401 4.8 35.2 1.0
CA A:MET49 4.8 48.3 1.0
C A:MET49 4.9 43.3 1.0
CB A:ARG188 4.9 35.1 1.0
CG A:GLN189 5.0 35.9 1.0

Fluorine binding site 4 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 4 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:48.2
occ:1.00
 F1 B:YDL401 0.0 48.2 1.0
C21 B:YDL401 1.4 48.9 1.0
F3 B:YDL401 2.2 52.5 1.0
F2 B:YDL401 2.3 45.0 1.0
C11 B:YDL401 2.4 48.7 1.0
C12 B:YDL401 2.8 44.1 1.0
CB B:HIS41 3.3 41.8 1.0
CG B:HIS41 3.6 43.1 1.0
OH B:TYR54 3.6 46.2 1.0
O B:ASP187 3.7 45.1 1.0
CD2 B:HIS41 3.7 39.8 1.0
C B:ASP187 3.8 44.5 1.0
C10 B:YDL401 3.9 47.5 1.0
C8 B:YDL401 4.0 41.0 1.0
CB B:ASP187 4.0 40.2 1.0
CA B:ASP187 4.2 44.6 1.0
N B:ARG188 4.3 44.2 1.0
ND1 B:HIS41 4.3 43.2 1.0
CG B:MET49 4.4 66.7 1.0
N3 B:YDL401 4.4 41.8 1.0
NE2 B:HIS41 4.6 43.8 1.0
CA B:ARG188 4.7 52.3 1.0
CA B:HIS41 4.8 43.4 1.0
SD B:MET49 4.8 79.7 1.0
CB B:MET49 4.9 64.9 1.0
CE1 B:HIS41 4.9 43.1 1.0
CZ B:TYR54 5.0 45.8 1.0
CG B:ASP187 5.0 43.3 1.0

Fluorine binding site 5 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 5 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.0
occ:1.00
 F2 B:YDL401 0.0 45.0 1.0
C21 B:YDL401 1.4 48.9 1.0
F3 B:YDL401 2.2 52.5 1.0
F1 B:YDL401 2.3 48.2 1.0
C11 B:YDL401 2.4 48.7 1.0
C12 B:YDL401 2.9 44.1 1.0
C10 B:YDL401 3.0 47.5 1.0
C8 B:YDL401 3.0 41.0 1.0
N3 B:YDL401 3.1 41.8 1.0
CB B:MET165 3.9 35.3 1.0
SD B:MET165 4.0 44.5 1.0
C13 B:YDL401 4.0 41.7 1.0
CA B:ASP187 4.1 44.6 1.0
C B:ASP187 4.1 44.5 1.0
N B:ARG188 4.1 44.2 1.0
CE B:MET165 4.3 46.8 1.0
CB B:ASP187 4.3 40.2 1.0
C9 B:YDL401 4.4 41.8 1.0
O B:HIS164 4.5 35.7 1.0
CG B:MET165 4.5 35.0 1.0
CD2 B:HIS41 4.5 39.8 1.0
C B:ARG188 4.6 50.1 1.0
O3 B:YDL401 4.6 38.6 1.0
O B:ASP187 4.6 45.1 1.0
O B:ARG188 4.7 51.0 1.0
CA B:ARG188 4.8 52.3 1.0
CA B:MET165 4.8 37.2 1.0
N B:GLN189 4.8 53.4 1.0
C14 B:YDL401 4.8 41.2 1.0
O4 B:YDL401 4.9 44.3 1.0
CG B:HIS41 5.0 43.1 1.0
NE2 B:HIS41 5.0 43.8 1.0

Fluorine binding site 6 out of 6 in 9bpf

Go back to Fluorine Binding Sites List in 9bpf
Fluorine binding site 6 out of 6 in the Crystal Structure of Main Protease of Sars-Cov-2 Complexed with Inhibitor


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 Main Protease of Sars-Cov-2 Complexed with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.5
occ:1.00
 F3 B:YDL401 0.0 52.5 1.0
C21 B:YDL401 1.4 48.9 1.0
F2 B:YDL401 2.2 45.0 1.0
F1 B:YDL401 2.2 48.2 1.0
C11 B:YDL401 2.4 48.7 1.0
N B:GLN189 3.0 53.4 1.0
C10 B:YDL401 3.1 47.5 1.0
C B:ARG188 3.1 50.1 1.0
N B:ARG188 3.3 44.2 1.0
CA B:ARG188 3.3 52.3 1.0
C B:ASP187 3.6 44.5 1.0
C12 B:YDL401 3.6 44.1 1.0
O B:ARG188 3.7 51.0 1.0
CA B:GLN189 3.7 54.2 1.0
O B:ASP187 3.8 45.1 1.0
CB B:GLN189 3.9 52.1 1.0
N3 B:YDL401 4.0 41.8 1.0
O B:MET49 4.1 58.2 1.0
CB B:MET49 4.3 64.9 1.0
C8 B:YDL401 4.3 41.0 1.0
CA B:ASP187 4.3 44.6 1.0
CG B:MET49 4.5 66.7 1.0
O4 B:YDL401 4.7 44.3 1.0
CA B:MET49 4.7 64.0 1.0
CE B:MET49 4.8 62.4 1.0
C B:MET49 4.8 61.5 1.0
OH B:TYR54 4.8 46.2 1.0
CB B:ARG188 4.9 48.2 1.0
CB B:ASP187 4.9 40.2 1.0

Reference:

P.Chen, T.J.Van Oers, E.Arutyunova, C.Fischer, C.Wang, T.Lamer, M.J.Van Belkum, H.S.Young, J.C.Vederas, M.J.Lemieux. A Structural Comparison of Oral Sars-Cov-2 Drug Candidate Ibuzatrelvir Complexed with the Main Protease (Mpro) of Sars-Cov-2 and Mers-Cov Jacs Au 2024.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.4C00508
Page generated: Wed Jul 16 10:38:56 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy