Atomistry » Fluorine » PDB 9ars-9cdk » 9bo4
Atomistry »
  Fluorine »
    PDB 9ars-9cdk »
      9bo4 »

Fluorine in PDB 9bo4: Crystal Structure of T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

Enzymatic activity of Crystal Structure of T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir

All present enzymatic activity of Crystal Structure of T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo4 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) 39.28 / 2.28
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.64, 53.7, 114.41, 90, 100.54, 90
R / Rfree (%) 19.4 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir (pdb code 9bo4). 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir, PDB code: 9bo4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 1 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:70.2
occ:1.00
 F1 A:4WI401 0.0 70.2 1.0
C22 A:4WI401 1.3 64.2 1.0
F2 A:4WI401 2.2 54.4 1.0
F3 A:4WI401 2.2 63.8 1.0
C21 A:4WI401 2.3 48.0 1.0
H16 A:4WI401 2.3 52.0 1.0
O A:GLU166 2.4 44.1 1.0
N4 A:4WI401 2.6 43.4 1.0
HE2 A:MET165 2.7 64.6 1.0
HE1 A:MET165 2.9 64.6 1.0
HB2 A:MET165 3.0 48.1 1.0
HA A:LEU167 3.0 56.9 1.0
HD23 A:LEU167 3.1 61.2 1.0
C A:GLU166 3.2 40.3 1.0
CE A:MET165 3.2 53.9 1.0
O4 A:4WI401 3.4 48.0 1.0
HG3 A:MET165 3.5 44.8 1.0
HG A:LEU167 3.6 57.1 1.0
H A:GLU166 3.6 45.7 1.0
N A:LEU167 3.8 38.3 1.0
HD21 A:LEU167 3.8 61.2 1.0
CA A:LEU167 3.8 47.4 1.0
CD2 A:LEU167 3.8 51.0 1.0
CB A:MET165 3.8 40.1 1.0
N A:GLU166 3.9 38.1 1.0
CG A:MET165 3.9 37.3 1.0
HE3 A:MET165 4.0 64.6 1.0
C14 A:4WI401 4.0 47.7 1.0
SD A:MET165 4.1 45.5 1.0
H18 A:4WI401 4.1 64.7 1.0
CG A:LEU167 4.1 47.6 1.0
CA A:GLU166 4.2 43.7 1.0
HD3 A:PRO168 4.3 71.7 1.0
O3 A:4WI401 4.4 48.6 1.0
HE21 A:GLN192 4.4 58.2 1.0
HB3 A:MET165 4.4 48.1 1.0
C13 A:4WI401 4.4 51.4 1.0
H22 A:4WI401 4.5 52.0 1.0
H A:LEU167 4.5 46.0 1.0
HE22 A:GLN192 4.5 58.2 1.0
CB A:LEU167 4.5 48.0 1.0
C A:MET165 4.5 35.9 1.0
H15 A:4WI401 4.6 57.3 1.0
NE2 A:GLN192 4.6 48.5 1.0
H26 A:4WI401 4.6 56.0 1.0
HB2 A:GLN192 4.6 60.7 1.0
HD22 A:LEU167 4.7 61.2 1.0
O A:HOH510 4.7 53.2 1.0
HA A:GLU166 4.7 52.5 1.0
CA A:MET165 4.8 41.0 1.0
HG2 A:MET165 4.9 44.8 1.0
C A:LEU167 5.0 57.1 1.0

Fluorine binding site 2 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 2 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.4
occ:1.00
 F2 A:4WI401 0.0 54.4 1.0
C22 A:4WI401 1.3 64.2 1.0
F1 A:4WI401 2.2 70.2 1.0
F3 A:4WI401 2.2 63.8 1.0
C21 A:4WI401 2.3 48.0 1.0
O4 A:4WI401 2.7 48.0 1.0
HE21 A:GLN192 2.7 58.2 1.0
HE2 A:MET165 2.7 64.6 1.0
NE2 A:GLN192 3.2 48.5 1.0
O A:THR190 3.3 50.9 1.0
HD23 A:LEU167 3.4 61.2 1.0
HB2 A:GLN192 3.4 60.7 1.0
HE22 A:GLN192 3.4 58.2 1.0
N4 A:4WI401 3.5 43.4 1.0
CE A:MET165 3.6 53.9 1.0
H A:THR190 3.7 53.4 1.0
H16 A:4WI401 3.7 52.0 1.0
HE1 A:MET165 3.8 64.6 1.0
O A:ARG188 3.9 40.5 1.0
HD21 A:LEU167 4.0 61.2 1.0
H A:GLN192 4.0 66.0 1.0
HA A:GLN189 4.0 52.6 1.0
HG3 A:GLN192 4.1 58.3 1.0
CD A:GLN192 4.1 44.7 1.0
HE3 A:MET165 4.1 64.6 1.0
CD2 A:LEU167 4.1 51.0 1.0
HA A:LEU167 4.1 56.9 1.0
CB A:GLN192 4.2 50.6 1.0
O A:GLU166 4.2 44.1 1.0
HD3 A:PRO168 4.3 71.7 1.0
CG A:GLN192 4.4 48.6 1.0
N A:THR190 4.4 44.5 1.0
C A:THR190 4.5 51.5 1.0
N A:GLN192 4.6 55.0 1.0
HB2 A:MET165 4.7 48.1 1.0
HD22 A:LEU167 4.7 61.2 1.0
C14 A:4WI401 4.8 47.7 1.0
SD A:MET165 4.8 45.5 1.0
H22 A:4WI401 4.8 52.0 1.0
H15 A:4WI401 4.9 57.3 1.0
HG A:LEU167 4.9 57.1 1.0
CA A:GLN189 4.9 43.9 1.0
CA A:GLN192 4.9 56.7 1.0
HB3 A:GLN192 4.9 60.7 1.0
O A:GLN192 5.0 52.9 1.0

Fluorine binding site 3 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 3 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:63.8
occ:1.00
 F3 A:4WI401 0.0 63.8 1.0
C22 A:4WI401 1.3 64.2 1.0
F2 A:4WI401 2.2 54.4 1.0
F1 A:4WI401 2.2 70.2 1.0
C21 A:4WI401 2.3 48.0 1.0
H16 A:4WI401 2.8 52.0 1.0
HA A:LEU167 2.8 56.9 1.0
O A:GLU166 2.8 44.1 1.0
HD3 A:PRO168 2.9 71.7 1.0
N4 A:4WI401 2.9 43.4 1.0
O A:HOH510 3.0 53.2 1.0
O4 A:4WI401 3.2 48.0 1.0
HD23 A:LEU167 3.3 61.2 1.0
H22 A:4WI401 3.4 52.0 1.0
CA A:LEU167 3.7 47.4 1.0
CD A:PRO168 3.8 59.7 1.0
C A:GLU166 3.9 40.3 1.0
H18 A:4WI401 4.1 64.7 1.0
HD2 A:PRO168 4.2 71.7 1.0
CD2 A:LEU167 4.2 51.0 1.0
N A:LEU167 4.2 38.3 1.0
C14 A:4WI401 4.3 47.7 1.0
C A:LEU167 4.3 57.1 1.0
HE2 A:MET165 4.3 64.6 1.0
C17 A:4WI401 4.4 43.4 1.0
N A:PRO168 4.4 62.9 1.0
O A:THR190 4.5 50.9 1.0
H A:GLN192 4.5 66.0 1.0
HB2 A:GLN192 4.5 60.7 1.0
HG3 A:PRO168 4.6 80.6 1.0
HD21 A:LEU167 4.6 61.2 1.0
H21 A:4WI401 4.6 52.0 1.0
H15 A:4WI401 4.7 57.3 1.0
HG A:LEU167 4.7 57.1 1.0
CB A:LEU167 4.7 48.0 1.0
HE1 A:MET165 4.8 64.6 1.0
CG A:PRO168 4.8 67.2 1.0
HE21 A:GLN192 4.8 58.2 1.0
C15 A:4WI401 4.8 46.2 1.0
HD22 A:LEU167 4.8 61.2 1.0
O A:GLN192 4.8 52.9 1.0
CG A:LEU167 4.8 47.6 1.0
HB3 A:LEU167 4.9 57.6 1.0
C16 A:4WI401 4.9 53.9 1.0
HB2 A:MET165 5.0 48.1 1.0
H A:GLU166 5.0 45.7 1.0

Fluorine binding site 4 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 4 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:58.8
occ:1.00
 F1 B:4WI401 0.0 58.8 1.0
C22 B:4WI401 1.3 65.0 1.0
H16 B:4WI401 2.1 57.9 1.0
F2 B:4WI401 2.2 59.3 1.0
F3 B:4WI401 2.2 65.6 1.0
C21 B:4WI401 2.3 50.1 1.0
O B:GLU166 2.3 44.9 1.0
HE2 B:MET165 2.5 64.5 1.0
HA B:LEU167 2.5 59.2 1.0
N4 B:4WI401 2.5 48.3 1.0
HD21 B:LEU167 2.5 52.7 1.0
C B:GLU166 3.2 40.9 1.0
CE B:MET165 3.3 53.8 1.0
HD23 B:LEU167 3.3 52.7 1.0
CD2 B:LEU167 3.3 43.9 1.0
CA B:LEU167 3.4 49.4 1.0
HD3 B:PRO168 3.4 76.7 1.0
O4 B:4WI401 3.5 44.3 1.0
HE1 B:MET165 3.5 64.5 1.0
N B:LEU167 3.6 49.5 1.0
HE3 B:MET165 3.6 64.5 1.0
HB2 B:MET165 3.7 52.4 1.0
HG3 B:MET165 3.8 48.0 1.0
H19 B:4WI401 3.9 60.6 1.0
C14 B:4WI401 4.0 45.9 1.0
HD22 B:LEU167 4.0 52.7 1.0
H B:GLU166 4.0 49.2 1.0
H21 B:4WI401 4.1 48.4 1.0
CD B:PRO168 4.3 63.9 1.0
N B:GLU166 4.3 41.0 1.0
CG B:LEU167 4.3 46.1 1.0
CB B:LEU167 4.3 48.2 1.0
C B:LEU167 4.3 57.2 1.0
CA B:GLU166 4.3 42.3 1.0
H B:LEU167 4.4 59.4 1.0
HG B:LEU167 4.4 55.3 1.0
CG B:MET165 4.4 40.0 1.0
C13 B:4WI401 4.5 44.4 1.0
O3 B:4WI401 4.5 44.0 1.0
CB B:MET165 4.5 43.7 1.0
HB2 B:GLN192 4.5 47.8 1.0
H15 B:4WI401 4.5 55.1 1.0
HB3 B:LEU167 4.5 57.8 1.0
HD2 B:PRO168 4.6 76.7 1.0
N B:PRO168 4.6 65.1 1.0
SD B:MET165 4.7 55.4 1.0
HE21 B:GLN192 4.8 59.5 1.0
C16 B:4WI401 4.8 50.5 1.0
C15 B:4WI401 4.8 46.3 1.0
HA B:GLU166 4.9 50.8 1.0
C17 B:4WI401 4.9 40.3 1.0

Fluorine binding site 5 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 5 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:59.3
occ:1.00
 F2 B:4WI401 0.0 59.3 1.0
C22 B:4WI401 1.3 65.0 1.0
F3 B:4WI401 2.2 65.6 1.0
F1 B:4WI401 2.2 58.8 1.0
C21 B:4WI401 2.3 50.1 1.0
O4 B:4WI401 2.7 44.3 1.0
HE2 B:MET165 2.8 64.5 1.0
HE21 B:GLN192 2.8 59.5 1.0
HE3 B:MET165 2.9 64.5 1.0
O B:THR190 3.0 47.5 1.0
CE B:MET165 3.1 53.8 1.0
HE1 B:MET165 3.1 64.5 1.0
NE2 B:GLN192 3.3 49.6 1.0
HB2 B:GLN192 3.4 47.8 1.0
N4 B:4WI401 3.4 48.3 1.0
HG3 B:GLN192 3.4 54.2 1.0
H16 B:4WI401 3.6 57.9 1.0
HE22 B:GLN192 3.7 59.5 1.0
H B:THR190 3.7 48.1 1.0
HD21 B:LEU167 3.7 52.7 1.0
HD23 B:LEU167 3.9 52.7 1.0
O B:ARG188 3.9 39.0 1.0
CD B:GLN192 3.9 38.6 1.0
H B:GLN192 3.9 67.0 1.0
CG B:GLN192 3.9 45.1 1.0
HD3 B:PRO168 4.0 76.7 1.0
CB B:GLN192 4.1 39.8 1.0
HA B:LEU167 4.2 59.2 1.0
C B:THR190 4.2 44.8 1.0
CD2 B:LEU167 4.2 43.9 1.0
HA B:GLN189 4.2 50.8 1.0
N B:GLN192 4.4 55.9 1.0
N B:THR190 4.4 40.1 1.0
O B:GLU166 4.5 44.9 1.0
HA B:ALA191 4.5 55.1 1.0
HD22 B:LEU167 4.5 52.7 1.0
C14 B:4WI401 4.7 45.9 1.0
HG23 B:THR190 4.7 53.5 1.0
H15 B:4WI401 4.7 55.1 1.0
HB2 B:MET165 4.8 52.4 1.0
HB3 B:GLN192 4.8 47.8 1.0
SD B:MET165 4.8 55.4 1.0
CA B:GLN192 4.8 46.9 1.0
OE1 B:GLN192 4.8 43.9 1.0
HG2 B:GLN192 4.9 54.2 1.0
H21 B:4WI401 4.9 48.4 1.0
CD B:PRO168 4.9 63.9 1.0
CA B:THR190 5.0 46.1 1.0
HG3 B:MET165 5.0 48.0 1.0
C B:ALA191 5.0 55.7 1.0

Fluorine binding site 6 out of 6 in 9bo4

Go back to Fluorine Binding Sites List in 9bo4
Fluorine binding site 6 out of 6 in the Crystal Structure of T21I 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 T21I Sars-Cov-2 Main Protease in Complex with Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:65.6
occ:1.00
 F3 B:4WI401 0.0 65.6 1.0
C22 B:4WI401 1.3 65.0 1.0
F2 B:4WI401 2.2 59.3 1.0
F1 B:4WI401 2.2 58.8 1.0
C21 B:4WI401 2.3 50.1 1.0
HD3 B:PRO168 2.5 76.7 1.0
O4 B:4WI401 3.0 44.3 1.0
N4 B:4WI401 3.1 48.3 1.0
H16 B:4WI401 3.1 57.9 1.0
HA B:LEU167 3.3 59.2 1.0
H21 B:4WI401 3.5 48.4 1.0
CD B:PRO168 3.5 63.9 1.0
HG3 B:PRO168 3.6 75.7 1.0
O B:GLU166 3.7 44.9 1.0
H B:GLN192 3.8 67.0 1.0
O B:THR190 3.9 47.5 1.0
HA B:ALA191 4.0 55.1 1.0
HD2 B:PRO168 4.1 76.7 1.0
CG B:PRO168 4.1 63.1 1.0
N B:PRO168 4.1 65.1 1.0
HD21 B:LEU167 4.2 52.7 1.0
HD23 B:LEU167 4.2 52.7 1.0
CA B:LEU167 4.2 49.4 1.0
HE2 B:MET165 4.2 64.5 1.0
HB2 B:GLN192 4.3 47.8 1.0
C17 B:4WI401 4.4 40.3 1.0
C14 B:4WI401 4.4 45.9 1.0
C B:LEU167 4.5 57.2 1.0
N B:GLN192 4.5 55.9 1.0
HG2 B:PRO168 4.6 75.7 1.0
H20 B:4WI401 4.6 48.4 1.0
CD2 B:LEU167 4.6 43.9 1.0
C B:GLU166 4.7 40.9 1.0
H15 B:4WI401 4.7 55.1 1.0
C B:THR190 4.7 44.8 1.0
H19 B:4WI401 4.7 60.6 1.0
HA B:PRO168 4.8 82.9 1.0
CA B:ALA191 4.8 46.0 1.0
HE21 B:GLN192 4.9 59.5 1.0
HG3 B:GLN192 4.9 54.2 1.0
H B:THR190 4.9 48.1 1.0
HE3 B:MET165 4.9 64.5 1.0
CE B:MET165 4.9 53.8 1.0
N B:LEU167 4.9 49.5 1.0
HE1 B:MET165 4.9 64.5 1.0
C15 B:4WI401 5.0 46.3 1.0
HB3 B:LEU167 5.0 57.8 1.0
CA B:PRO168 5.0 69.1 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: Wed Jul 16 10:37:10 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