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

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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

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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

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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

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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: Sun Aug 11 11:25:54 2024

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