Fluorine in PDB 7tll: Structure of Sars-Cov-2 Mpro Omicron P132H in Complex with Nirmatrelvir (Pf-07321332)

Enzymatic activity of Structure of Sars-Cov-2 Mpro Omicron P132H in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro Omicron P132H in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro Omicron P132H in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7tll was solved by S.E.Greasley, R.A.Ferre, O.Plotnikova, W.Liu, A.E.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.84 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.39, 53.815, 115.538, 90, 102.42, 90
R / Rfree (%) 21.1 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Mpro Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) (pdb code 7tll). 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7tll:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7tll

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Fluorine binding site 1 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.7
occ:1.00
 F1 A:4WI401 0.0 32.7 1.0
C22 A:4WI401 1.4 31.1 1.0
F3 A:4WI401 2.1 32.0 1.0
F2 A:4WI401 2.2 32.5 1.0
C21 A:4WI401 2.4 27.2 1.0
N4 A:4WI401 2.7 23.3 1.0
O A:GLU166 2.8 22.4 1.0
CE A:MET165 2.8 29.6 1.0
C A:GLU166 3.4 22.4 1.0
O4 A:4WI401 3.5 27.0 1.0
CD2 A:LEU167 3.6 28.8 1.0
CA A:LEU167 3.7 26.5 1.0
CB A:MET165 3.8 18.6 1.0
N A:LEU167 3.8 24.2 1.0
CG A:MET165 3.9 22.2 1.0
SD A:MET165 4.0 27.9 1.0
CG A:LEU167 4.0 28.4 1.0
C14 A:4WI401 4.1 21.1 1.0
N A:GLU166 4.1 18.6 1.0
O3 A:4WI401 4.2 20.3 1.0
C13 A:4WI401 4.3 20.6 1.0
CA A:GLU166 4.4 19.4 1.0
O A:HOH623 4.5 41.9 1.0
CB A:LEU167 4.5 27.0 1.0
NE2 A:GLN192 4.7 23.3 1.0
C A:MET165 4.7 18.0 1.0
CD A:PRO168 4.8 31.7 1.0
C A:LEU167 4.8 29.2 1.0
CA A:MET165 4.9 17.2 1.0

Fluorine binding site 2 out of 6 in 7tll

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Fluorine binding site 2 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.5
occ:1.00
 F2 A:4WI401 0.0 32.5 1.0
C22 A:4WI401 1.4 31.1 1.0
F1 A:4WI401 2.2 32.7 1.0
F3 A:4WI401 2.2 32.0 1.0
C21 A:4WI401 2.4 27.2 1.0
O4 A:4WI401 2.7 27.0 1.0
O A:THR190 2.9 26.0 1.0
NE2 A:GLN192 3.2 23.3 1.0
CE A:MET165 3.4 29.6 1.0
N4 A:4WI401 3.6 23.3 1.0
O A:ARG188 3.8 20.8 1.0
CD A:GLN192 3.9 24.0 1.0
C A:THR190 4.0 26.2 1.0
CG A:GLN192 4.1 23.2 1.0
CB A:GLN192 4.2 23.9 1.0
N A:THR190 4.2 24.3 1.0
CD2 A:LEU167 4.3 28.8 1.0
N A:GLN192 4.5 25.3 1.0
O A:GLU166 4.7 22.4 1.0
C14 A:4WI401 4.7 21.1 1.0
OE1 A:GLN192 4.8 23.5 1.0
SD A:MET165 4.8 27.9 1.0
CA A:THR190 4.8 25.7 1.0
N A:ALA191 4.9 26.6 1.0
C A:ARG188 4.9 20.9 1.0
CA A:GLN189 4.9 21.9 1.0
CA A:ALA191 4.9 26.9 1.0
C A:ALA191 4.9 26.2 1.0
CD A:PRO168 5.0 31.7 1.0
CA A:GLN192 5.0 25.1 1.0

Fluorine binding site 3 out of 6 in 7tll

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Fluorine binding site 3 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.0
occ:1.00
 F3 A:4WI401 0.0 32.0 1.0
C22 A:4WI401 1.3 31.1 1.0
F1 A:4WI401 2.1 32.7 1.0
F2 A:4WI401 2.2 32.5 1.0
C21 A:4WI401 2.3 27.2 1.0
N4 A:4WI401 3.0 23.3 1.0
O A:HOH623 3.1 41.9 1.0
O4 A:4WI401 3.2 27.0 1.0
O A:GLU166 3.2 22.4 1.0
CD A:PRO168 3.3 31.7 1.0
CA A:LEU167 3.6 26.5 1.0
N A:PRO168 3.9 31.6 1.0
CG A:PRO168 3.9 34.3 1.0
C A:LEU167 4.0 29.2 1.0
C A:GLU166 4.1 22.4 1.0
CD2 A:LEU167 4.1 28.8 1.0
O A:THR190 4.2 26.0 1.0
N A:LEU167 4.3 24.2 1.0
C14 A:4WI401 4.3 21.1 1.0
CB A:LEU167 4.6 27.0 1.0
CE A:MET165 4.7 29.6 1.0
CG A:LEU167 4.7 28.4 1.0
N A:GLN192 4.8 25.3 1.0
C16 A:4WI401 4.8 20.8 1.0
CA A:PRO168 4.8 33.6 1.0
O A:LEU167 5.0 28.8 1.0

Fluorine binding site 4 out of 6 in 7tll

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Fluorine binding site 4 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:32.4
occ:1.00
 F1 B:4WI401 0.0 32.4 1.0
C22 B:4WI401 1.4 31.5 1.0
F2 B:4WI401 2.1 33.1 1.0
F3 B:4WI401 2.2 32.3 1.0
C21 B:4WI401 2.4 28.4 1.0
N4 B:4WI401 2.7 23.6 1.0
O B:GLU166 2.8 19.3 1.0
CE B:MET165 2.8 33.1 1.0
C B:GLU166 3.4 20.4 1.0
O4 B:4WI401 3.5 29.5 1.0
CD2 B:LEU167 3.5 27.8 1.0
CB B:MET165 3.7 18.5 1.0
CG B:MET165 3.8 21.3 1.0
CA B:LEU167 3.9 24.0 1.0
N B:LEU167 3.9 21.7 1.0
SD B:MET165 3.9 29.1 1.0
N B:GLU166 4.1 17.3 1.0
C14 B:4WI401 4.1 21.0 1.0
O3 B:4WI401 4.3 19.0 1.0
C13 B:4WI401 4.3 19.8 1.0
CA B:GLU166 4.4 18.2 1.0
CG B:LEU167 4.5 26.6 1.0
C B:MET165 4.6 17.3 1.0
NE2 B:GLN192 4.7 23.0 1.0
CB B:LEU167 4.7 24.6 1.0
CA B:MET165 4.8 17.3 1.0
CD B:PRO168 4.9 28.0 1.0
C B:LEU167 4.9 26.6 1.0
O B:THR190 4.9 23.0 1.0

Fluorine binding site 5 out of 6 in 7tll

Go back to Fluorine Binding Sites List in 7tll
Fluorine binding site 5 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.1
occ:1.00
 F2 B:4WI401 0.0 33.1 1.0
C22 B:4WI401 1.4 31.5 1.0
F1 B:4WI401 2.1 32.4 1.0
F3 B:4WI401 2.2 32.3 1.0
C21 B:4WI401 2.4 28.4 1.0
O4 B:4WI401 2.7 29.5 1.0
O B:THR190 2.9 23.0 1.0
NE2 B:GLN192 3.1 23.0 1.0
CE B:MET165 3.2 33.1 1.0
N4 B:4WI401 3.5 23.6 1.0
O B:ARG188 3.6 20.0 1.0
CD B:GLN192 3.9 24.3 1.0
C B:THR190 4.0 23.0 1.0
N B:THR190 4.1 21.4 1.0
CG B:GLN192 4.2 22.7 1.0
CB B:GLN192 4.4 21.3 1.0
CD2 B:LEU167 4.5 27.8 1.0
SD B:MET165 4.5 29.1 1.0
N B:GLN192 4.6 21.6 1.0
O B:GLU166 4.6 19.3 1.0
CA B:THR190 4.7 22.5 1.0
C14 B:4WI401 4.7 21.0 1.0
C B:ARG188 4.7 19.9 1.0
CA B:GLN189 4.8 19.9 1.0
OE1 B:GLN192 4.8 25.3 1.0
N B:ALA191 4.9 22.9 1.0
C B:GLN189 4.9 20.9 1.0
CA B:ALA191 4.9 23.2 1.0
C B:ALA191 5.0 22.2 1.0

Fluorine binding site 6 out of 6 in 7tll

Go back to Fluorine Binding Sites List in 7tll
Fluorine binding site 6 out of 6 in the Structure of Sars-Cov-2 Mpro Omicron P132H 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 Omicron P132H in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:32.3
occ:1.00
 F3 B:4WI401 0.0 32.3 1.0
C22 B:4WI401 1.3 31.5 1.0
F1 B:4WI401 2.2 32.4 1.0
F2 B:4WI401 2.2 33.1 1.0
C21 B:4WI401 2.3 28.4 1.0
N4 B:4WI401 3.0 23.6 1.0
O4 B:4WI401 3.1 29.5 1.0
O B:GLU166 3.2 19.3 1.0
CD B:PRO168 3.3 28.0 1.0
CA B:LEU167 3.8 24.0 1.0
O B:THR190 3.9 23.0 1.0
CG B:PRO168 4.0 30.2 1.0
N B:PRO168 4.0 28.2 1.0
CD2 B:LEU167 4.1 27.8 1.0
C B:GLU166 4.2 20.4 1.0
C B:LEU167 4.2 26.6 1.0
N B:LEU167 4.4 21.7 1.0
C14 B:4WI401 4.4 21.0 1.0
N B:GLN192 4.5 21.6 1.0
CE B:MET165 4.6 33.1 1.0
C B:THR190 4.7 23.0 1.0
CB B:LEU167 4.8 24.6 1.0
CA B:ALA191 4.8 23.2 1.0
C16 B:4WI401 4.9 19.6 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 13:30:09 2024

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