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Fluorine in PDB 9bo5: Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo5 was solved by C.Papini, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.10 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.664, 98.671, 59.244, 90, 107.9, 90
R / Rfree (%) 19.3 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir (pdb code 9bo5). 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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 1 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.2
occ:1.00
 F1 A:4WI401 0.0 41.2 1.0
C22 A:4WI401 1.3 37.7 1.0
F2 A:4WI401 2.2 43.8 1.0
F3 A:4WI401 2.2 48.0 1.0
H16 A:4WI401 2.2 33.5 1.0
C21 A:4WI401 2.3 34.3 1.0
N4 A:4WI401 2.6 27.9 1.0
O A:GLU166 2.6 26.7 1.0
CE A:MET165 3.4 33.3 1.0
C A:GLU166 3.4 27.8 1.0
O4 A:4WI401 3.5 32.5 1.0
CD2 A:LEU167 3.5 36.2 1.0
CA A:LEU167 3.5 31.6 1.0
N A:LEU167 3.8 24.2 1.0
H19 A:4WI401 3.9 39.1 1.0
C14 A:4WI401 4.0 30.6 1.0
CD A:PRO168 4.2 32.6 1.0
H21 A:4WI401 4.3 37.9 1.0
N A:GLU166 4.4 24.8 1.0
CG A:LEU167 4.4 30.2 1.0
CB A:LEU167 4.4 30.0 1.0
C A:LEU167 4.4 38.2 1.0
C13 A:4WI401 4.5 31.0 1.0
O3 A:4WI401 4.5 24.7 1.0
CA A:GLU166 4.5 28.0 1.0
CB A:MET165 4.6 25.1 1.0
H15 A:4WI401 4.6 36.7 1.0
CG A:MET165 4.6 30.2 1.0
N A:PRO168 4.7 38.7 1.0
O A:ILE190 4.8 29.3 1.0
SD A:MET165 4.8 38.5 1.0
C16 A:4WI401 4.8 32.6 1.0
C15 A:4WI401 4.9 35.3 1.0
C17 A:4WI401 4.9 31.5 1.0
NE2 A:GLN192 5.0 24.4 1.0

Fluorine binding site 2 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 2 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:43.8
occ:1.00
 F2 A:4WI401 0.0 43.8 1.0
C22 A:4WI401 1.3 37.7 1.0
F1 A:4WI401 2.2 41.2 1.0
F3 A:4WI401 2.2 48.0 1.0
C21 A:4WI401 2.3 34.3 1.0
O4 A:4WI401 2.7 32.5 1.0
O A:ILE190 2.8 29.3 1.0
CE A:MET165 3.1 33.3 1.0
NE2 A:GLN192 3.3 24.4 1.0
N4 A:4WI401 3.4 27.9 1.0
H16 A:4WI401 3.6 33.5 1.0
CG A:GLN192 3.8 30.8 1.0
CD A:GLN192 3.8 28.7 1.0
C A:ILE190 3.9 36.5 1.0
O A:ARG188 4.0 25.7 1.0
CB A:GLN192 4.0 28.4 1.0
N A:GLN192 4.1 31.9 1.0
N A:ILE190 4.2 34.8 1.0
H27 A:4WI401 4.4 32.2 1.0
CD2 A:LEU167 4.5 36.2 1.0
C A:ALA191 4.6 35.0 1.0
C14 A:4WI401 4.6 30.6 1.0
CA A:GLN192 4.7 32.4 1.0
O A:GLU166 4.7 26.7 1.0
H15 A:4WI401 4.7 36.7 1.0
CA A:ALA191 4.7 44.0 1.0
CA A:ILE190 4.8 34.5 0.5
CA A:ILE190 4.8 34.5 0.5
N A:ALA191 4.8 36.8 1.0
OE1 A:GLN192 4.8 24.2 1.0
O A:HOH592 4.9 41.8 1.0
SD A:MET165 4.9 38.5 1.0
H11 A:4WI401 5.0 37.2 1.0
CA A:GLN189 5.0 29.9 1.0

Fluorine binding site 3 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 3 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:48.0
occ:1.00
 F3 A:4WI401 0.0 48.0 1.0
C22 A:4WI401 1.3 37.7 1.0
F1 A:4WI401 2.2 41.2 1.0
F2 A:4WI401 2.2 43.8 1.0
C21 A:4WI401 2.3 34.3 1.0
O4 A:4WI401 3.0 32.5 1.0
N4 A:4WI401 3.2 27.9 1.0
H16 A:4WI401 3.2 33.5 1.0
O A:ILE190 3.6 29.3 1.0
CD A:PRO168 3.6 32.6 1.0
H21 A:4WI401 3.7 37.9 1.0
O A:HOH592 3.7 41.8 1.0
CG A:PRO168 3.9 35.5 1.0
O A:GLU166 3.9 26.7 1.0
N A:GLN192 4.0 31.9 1.0
CA A:ALA191 4.3 44.0 1.0
C A:ILE190 4.4 36.5 1.0
H20 A:4WI401 4.4 37.9 1.0
N A:PRO168 4.4 38.7 1.0
CA A:LEU167 4.5 31.6 1.0
C17 A:4WI401 4.5 31.5 1.0
C14 A:4WI401 4.5 30.6 1.0
O A:GLN192 4.5 42.2 1.0
C A:ALA191 4.6 35.0 1.0
H19 A:4WI401 4.7 39.1 1.0
CD2 A:LEU167 4.7 36.2 1.0
H15 A:4WI401 4.7 36.7 1.0
N A:ALA191 4.7 36.8 1.0
C A:LEU167 4.8 38.2 1.0
CB A:GLN192 4.9 28.4 1.0
CA A:GLN192 4.9 32.4 1.0
CE A:MET165 4.9 33.3 1.0
C A:GLU166 4.9 27.8 1.0

Fluorine binding site 4 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 4 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.2
occ:1.00
 F1 B:4WI401 0.0 37.2 1.0
C22 B:4WI401 1.3 38.0 1.0
F3 B:4WI401 2.2 41.0 1.0
F2 B:4WI401 2.2 45.7 1.0
C21 B:4WI401 2.4 36.5 1.0
H16 B:4WI401 2.4 34.8 1.0
O B:GLU166 2.6 28.4 1.0
N4 B:4WI401 2.7 28.9 1.0
CE B:MET165 3.1 32.8 1.0
C B:GLU166 3.4 30.2 1.0
O4 B:4WI401 3.4 33.6 1.0
CA B:LEU167 3.6 27.9 1.0
CD2 B:LEU167 3.7 33.0 1.0
N B:LEU167 3.8 27.5 1.0
O B:HOH540 4.0 39.7 1.0
H18 B:4WI401 4.1 38.9 1.0
C14 B:4WI401 4.1 26.5 1.0
CG B:LEU167 4.2 31.6 1.0
N B:GLU166 4.3 23.0 1.0
CB B:MET165 4.4 25.4 1.0
CG B:MET165 4.4 27.4 1.0
CA B:GLU166 4.5 24.4 1.0
CB B:LEU167 4.5 28.2 1.0
O3 B:4WI401 4.5 26.8 1.0
SD B:MET165 4.5 36.0 1.0
CD B:PRO168 4.5 35.5 1.0
C13 B:4WI401 4.5 27.9 1.0
H20 B:4WI401 4.5 34.2 1.0
C B:LEU167 4.6 33.6 1.0
H15 B:4WI401 4.7 31.9 1.0
H28 B:4WI401 4.8 34.4 1.0
CB B:GLN192 4.9 35.1 1.0
N B:PRO168 4.9 36.0 1.0
C16 B:4WI401 4.9 32.4 1.0

Fluorine binding site 5 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 5 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:45.7
occ:1.00
 F2 B:4WI401 0.0 45.7 1.0
C22 B:4WI401 1.3 38.0 1.0
F1 B:4WI401 2.2 37.2 1.0
F3 B:4WI401 2.2 41.0 1.0
C21 B:4WI401 2.3 36.5 1.0
O4 B:4WI401 2.7 33.6 1.0
O B:ILE190 3.0 33.0 1.0
N4 B:4WI401 3.5 28.9 1.0
CE B:MET165 3.5 32.8 1.0
NE2 B:GLN192 3.6 30.1 1.0
CB B:GLN192 3.7 35.1 1.0
H16 B:4WI401 3.7 34.8 1.0
N B:GLN192 4.0 35.9 1.0
CG B:GLN192 4.0 35.5 1.0
CD B:GLN192 4.0 33.4 1.0
C B:ILE190 4.1 38.8 1.0
O B:ARG188 4.3 30.2 1.0
CA B:GLN192 4.4 29.9 1.0
N B:ILE190 4.5 34.2 1.0
CD2 B:LEU167 4.5 33.0 1.0
O B:GLU166 4.6 28.4 1.0
C B:ALA191 4.7 33.6 1.0
O B:GLN192 4.7 36.7 1.0
C14 B:4WI401 4.8 26.5 1.0
H28 B:4WI401 4.8 34.4 1.0
H15 B:4WI401 4.8 31.9 1.0
OE1 B:GLN192 4.9 32.9 1.0
H20 B:4WI401 4.9 34.2 1.0
CA B:ALA191 5.0 39.9 1.0
C B:GLN192 5.0 28.6 1.0
N B:ALA191 5.0 37.0 1.0

Fluorine binding site 6 out of 6 in 9bo5

Go back to Fluorine Binding Sites List in 9bo5
Fluorine binding site 6 out of 6 in the Crystal Structure of T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir


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 T190I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:41.0
occ:1.00
 F3 B:4WI401 0.0 41.0 1.0
C22 B:4WI401 1.3 38.0 1.0
F1 B:4WI401 2.2 37.2 1.0
F2 B:4WI401 2.2 45.7 1.0
C21 B:4WI401 2.3 36.5 1.0
H16 B:4WI401 2.8 34.8 1.0
N4 B:4WI401 2.9 28.9 1.0
O B:HOH540 3.0 39.7 1.0
O4 B:4WI401 3.2 33.6 1.0
O B:GLU166 3.4 28.4 1.0
H20 B:4WI401 3.4 34.2 1.0
CD B:PRO168 3.5 35.5 1.0
CG B:PRO168 4.0 34.9 1.0
CA B:LEU167 4.1 27.9 1.0
N B:PRO168 4.2 36.0 1.0
C14 B:4WI401 4.3 26.5 1.0
C B:GLU166 4.4 30.2 1.0
C B:LEU167 4.4 33.6 1.0
C17 B:4WI401 4.4 28.5 1.0
O B:ILE190 4.5 33.0 1.0
H18 B:4WI401 4.5 38.9 1.0
O B:GLN192 4.5 36.7 1.0
H15 B:4WI401 4.6 31.9 1.0
H22 B:4WI401 4.6 34.2 1.0
N B:GLN192 4.7 35.9 1.0
N B:LEU167 4.7 27.5 1.0
CD2 B:LEU167 4.7 33.0 1.0
H17 B:4WI401 4.8 38.9 1.0
C15 B:4WI401 4.8 30.7 1.0
C16 B:4WI401 4.9 32.4 1.0
CE B:MET165 5.0 32.8 1.0

Reference:

J.R.Kenneson, C.Papini, S.Tang, K.Huynh, C.H.Zhang, W.L.Jorgensen, K.S.Anderson. Exploring Possible Drug-Resistant Variants of Sars-Cov-2 Main Protease (Mpro) with Noncovalent Preclinical Candidate, MPRO61 Acs Bio Med Chem Au 2025.
ISSN: ESSN 2694-2437
DOI: 10.1021/ACSBIOMEDCHEMAU.4C00109
Page generated: Tue Feb 25 09:29:41 2025

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