Fluorine in PDB 7u29: Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)

Enzymatic activity of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7u29 was solved by S.E.Greasley, R.A.Ferre, W.Liu, A.E.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.22 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.52, 55.786, 114.225, 90, 105.22, 90
R / Rfree (%) 20.4 / 26.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) (pdb code 7u29). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7u29:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u29

Go back to Fluorine Binding Sites List in 7u29
Fluorine binding site 1 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.1
occ:1.00
 F1 A:4WI401 0.0 35.1 1.0
C22 A:4WI401 1.4 34.8 1.0
F2 A:4WI401 2.2 35.5 1.0
F3 A:4WI401 2.2 35.6 1.0
C21 A:4WI401 2.4 32.9 1.0
N4 A:4WI401 2.8 30.7 1.0
O A:GLU166 2.9 25.5 1.0
CE A:MET165 3.3 35.1 1.0
O4 A:4WI401 3.4 33.1 1.0
CD2 A:LEU167 3.6 30.8 1.0
C A:GLU166 3.6 25.1 1.0
CA A:LEU167 3.6 29.0 1.0
CG A:LEU167 3.9 30.5 1.0
N A:LEU167 3.9 26.6 1.0
C14 A:4WI401 4.3 28.9 1.0
CB A:LEU167 4.3 29.3 1.0
CD A:PRO168 4.5 33.9 1.0
CB A:GLN192 4.6 31.0 1.0
C A:LEU167 4.6 32.5 1.0
O3 A:4WI401 4.7 29.0 1.0
CG A:MET165 4.7 24.7 1.0
N A:GLU166 4.7 21.2 1.0
SD A:MET165 4.7 35.3 1.0
O A:GLN192 4.8 31.0 1.0
C13 A:4WI401 4.8 28.7 1.0
CA A:GLU166 4.8 22.6 1.0
CB A:MET165 4.8 21.5 1.0
NE2 A:GLN192 4.9 30.1 1.0
N A:PRO168 4.9 34.3 1.0
O A:THR190 4.9 35.0 1.0

Fluorine binding site 2 out of 6 in 7u29

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Fluorine binding site 2 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:1.00
 F2 A:4WI401 0.0 35.5 1.0
C22 A:4WI401 1.4 34.8 1.0
F1 A:4WI401 2.2 35.1 1.0
F3 A:4WI401 2.2 35.6 1.0
C21 A:4WI401 2.3 32.9 1.0
O4 A:4WI401 2.6 33.1 1.0
O A:THR190 2.8 35.0 1.0
N4 A:4WI401 3.5 30.7 1.0
CE A:MET165 3.6 35.1 1.0
NE2 A:GLN192 3.6 30.1 1.0
CB A:GLN192 3.8 31.0 1.0
C A:THR190 4.0 34.2 1.0
CG A:GLN192 4.0 31.0 1.0
O A:ARG188 4.0 24.6 1.0
N A:GLN192 4.1 31.6 1.0
N A:THR190 4.1 31.3 1.0
CD A:GLN192 4.2 31.8 1.0
CA A:GLN192 4.5 31.3 1.0
O A:GLN192 4.6 31.0 1.0
CD2 A:LEU167 4.7 30.8 1.0
CA A:THR190 4.7 33.2 1.0
C14 A:4WI401 4.8 28.9 1.0
O A:GLU166 4.8 25.5 1.0
C A:ALA191 4.9 32.8 1.0
CA A:GLN189 4.9 27.9 1.0
C A:GLN189 4.9 30.4 1.0
N A:ALA191 5.0 33.8 1.0

Fluorine binding site 3 out of 6 in 7u29

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Fluorine binding site 3 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.6
occ:1.00
 F3 A:4WI401 0.0 35.6 1.0
C22 A:4WI401 1.4 34.8 1.0
F1 A:4WI401 2.2 35.1 1.0
F2 A:4WI401 2.2 35.5 1.0
C21 A:4WI401 2.4 32.9 1.0
N4 A:4WI401 3.1 30.7 1.0
O4 A:4WI401 3.2 33.1 1.0
O A:GLU166 3.8 25.5 1.0
CD A:PRO168 4.1 33.9 1.0
O A:THR190 4.2 35.0 1.0
C14 A:4WI401 4.3 28.9 1.0
O A:GLN192 4.4 31.0 1.0
CA A:LEU167 4.4 29.0 1.0
C16 A:4WI401 4.5 27.2 1.0
CG A:PRO168 4.5 36.1 1.0
N A:PRO168 4.6 34.3 1.0
N A:GLN192 4.7 31.6 1.0
C A:GLU166 4.8 25.1 1.0
C A:LEU167 4.8 32.5 1.0
CD2 A:LEU167 4.8 30.8 1.0
C15 A:4WI401 4.9 27.5 1.0

Fluorine binding site 4 out of 6 in 7u29

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Fluorine binding site 4 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:38.0
occ:1.00
 F1 B:4WI401 0.0 38.0 1.0
C22 B:4WI401 1.4 37.4 1.0
F2 B:4WI401 2.1 38.2 1.0
F3 B:4WI401 2.2 37.6 1.0
C21 B:4WI401 2.4 35.4 1.0
N4 B:4WI401 2.8 33.2 1.0
O B:GLU166 2.8 28.2 1.0
CE B:MET165 3.2 34.8 1.0
C B:GLU166 3.4 27.8 1.0
O4 B:4WI401 3.5 35.4 1.0
CD2 B:LEU167 3.7 33.7 1.0
CA B:LEU167 3.8 31.6 1.0
N B:LEU167 3.9 29.5 1.0
CG B:MET165 4.0 24.3 1.0
SD B:MET165 4.1 33.9 1.0
CB B:MET165 4.1 21.0 1.0
C14 B:4WI401 4.1 31.6 1.0
N B:GLU166 4.2 23.2 1.0
CG B:LEU167 4.3 32.8 1.0
O3 B:4WI401 4.3 30.7 1.0
C13 B:4WI401 4.4 30.6 1.0
NE2 B:GLN192 4.4 25.6 1.0
CA B:GLU166 4.5 24.8 1.0
CB B:LEU167 4.6 31.5 1.0
C B:MET165 4.8 21.9 1.0
C B:LEU167 4.9 34.5 1.0
O B:THR190 4.9 28.7 1.0
CD B:PRO168 4.9 36.1 1.0

Fluorine binding site 5 out of 6 in 7u29

Go back to Fluorine Binding Sites List in 7u29
Fluorine binding site 5 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:38.2
occ:1.00
 F2 B:4WI401 0.0 38.2 1.0
C22 B:4WI401 1.4 37.4 1.0
F1 B:4WI401 2.1 38.0 1.0
F3 B:4WI401 2.2 37.6 1.0
C21 B:4WI401 2.4 35.4 1.0
O4 B:4WI401 2.7 35.4 1.0
O B:THR190 2.8 28.7 1.0
NE2 B:GLN192 3.0 25.6 1.0
N4 B:4WI401 3.6 33.2 1.0
O B:ARG188 3.8 23.2 1.0
C B:THR190 3.9 28.3 1.0
CE B:MET165 3.9 34.8 1.0
CD B:GLN192 3.9 28.2 1.0
N B:THR190 4.1 25.3 1.0
CB B:GLN192 4.4 29.1 1.0
N B:GLN192 4.4 29.1 1.0
CG B:GLN192 4.4 29.0 1.0
CD2 B:LEU167 4.5 33.7 1.0
CA B:THR190 4.7 27.0 1.0
O B:GLU166 4.7 28.2 1.0
N B:ALA191 4.7 28.4 1.0
OE1 B:GLN192 4.8 30.0 1.0
C14 B:4WI401 4.8 31.6 1.0
SD B:MET165 4.8 33.9 1.0
CA B:ALA191 4.8 28.9 1.0
C B:ALA191 4.9 29.2 1.0
CA B:GLN189 4.9 22.4 1.0
C B:GLN189 5.0 24.8 1.0
C B:ARG188 5.0 22.3 1.0

Fluorine binding site 6 out of 6 in 7u29

Go back to Fluorine Binding Sites List in 7u29
Fluorine binding site 6 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Sars-Cov-2 Mpro Mutant (K90R) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.6
occ:1.00
 F3 B:4WI401 0.0 37.6 1.0
C22 B:4WI401 1.4 37.4 1.0
F1 B:4WI401 2.2 38.0 1.0
F2 B:4WI401 2.2 38.2 1.0
C21 B:4WI401 2.4 35.4 1.0
N4 B:4WI401 3.1 33.2 1.0
O4 B:4WI401 3.2 35.4 1.0
O B:GLU166 3.3 28.2 1.0
CD B:PRO168 3.6 36.1 1.0
CA B:LEU167 3.8 31.6 1.0
N B:PRO168 4.1 36.2 1.0
O B:THR190 4.1 28.7 1.0
C B:LEU167 4.2 34.5 1.0
CG B:PRO168 4.2 38.2 1.0
C B:GLU166 4.2 27.8 1.0
CD2 B:LEU167 4.3 33.7 1.0
N B:LEU167 4.4 29.5 1.0
C14 B:4WI401 4.4 31.6 1.0
N B:GLN192 4.7 29.1 1.0
C16 B:4WI401 4.7 31.3 1.0
CB B:LEU167 4.8 31.5 1.0
C B:THR190 4.9 28.3 1.0
O B:GLN192 4.9 30.2 1.0
CA B:ALA191 5.0 28.9 1.0
CA B:PRO168 5.0 37.1 1.0

Reference:

S.E.Greasley, S.Noell, O.Plotnikova, R.Ferre, W.Liu, B.Bolanos, K.Fennell, J.Nicki, T.Craig, Y.Zhu, A.E.Stewart, C.M.Steppan. Structural Basis For the in Vitro Efficacy of Nirmatrelvir Against Sars-Cov-2 Variants. J.Biol.Chem. V. 298 01972 2022.
ISSN: ESSN 1083-351X
PubMed: 35461811
DOI: 10.1016/J.JBC.2022.101972
Page generated: Fri Aug 2 13:50:50 2024

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