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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: Tue Feb 25 09:29:44 2025

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