Fluorine in PDB 9auk: Structure of Sars-Cov-2 Mpro Mutant (A173V) in Complex with Nirmatrelvir (Pf-07321332)

Enzymatic activity of Structure of Sars-Cov-2 Mpro Mutant (A173V) in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro Mutant (A173V) in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro Mutant (A173V) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 9auk was solved by K.S.Gajiwala, 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) 112.67 / 1.88
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.475, 54.569, 114.929, 90, 101.37, 90
R / Rfree (%) 20.7 / 25.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Mpro Mutant (A173V) in Complex with Nirmatrelvir (Pf-07321332) (pdb code 9auk). 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 9auk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9auk

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Fluorine binding site 1 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.4
occ:1.00
 F1 A:4WI401 0.0 38.4 1.0
C22 A:4WI401 1.4 37.4 1.0
F2 A:4WI401 2.2 38.2 1.0
F3 A:4WI401 2.2 36.6 1.0
C21 A:4WI401 2.4 36.1 1.0
H16 A:4WI401 2.5 35.4 0.0
N4 A:4WI401 2.9 35.4 1.0
O A:GLU166 2.9 33.7 1.0
CE A:MET165 3.1 35.1 1.0
O4 A:4WI401 3.4 35.6 1.0
C A:GLU166 3.4 34.4 1.0
SD A:MET165 3.5 35.7 1.0
CD2 A:LEU167 3.8 38.0 1.0
CB A:MET165 3.8 31.9 1.0
CA A:LEU167 3.9 37.0 1.0
N A:LEU167 3.9 35.8 1.0
CG A:MET165 4.0 34.6 1.0
N A:GLU166 4.1 31.5 1.0
C14 A:4WI401 4.2 34.6 1.0
CA A:GLU166 4.4 32.7 1.0
O3 A:4WI401 4.4 35.5 1.0
C13 A:4WI401 4.5 34.7 1.0
C A:MET165 4.6 30.7 1.0
CG A:LEU167 4.6 37.8 1.0
H15 A:4WI401 4.7 34.6 0.0
H25 A:4WI401 4.7 33.3 0.0
H30 A:4WI401 4.8 33.3 0.0
NE2 A:GLN192 4.8 36.2 1.0
CB A:LEU167 4.8 36.6 1.0
CA A:MET165 4.9 30.0 1.0
C A:LEU167 4.9 39.0 1.0
CD A:PRO168 4.9 39.4 1.0
O A:THR190 5.0 34.6 1.0

Fluorine binding site 2 out of 6 in 9auk

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Fluorine binding site 2 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:38.2
occ:1.00
 F2 A:4WI401 0.0 38.2 1.0
C22 A:4WI401 1.4 37.4 1.0
F3 A:4WI401 2.1 36.6 1.0
F1 A:4WI401 2.2 38.4 1.0
C21 A:4WI401 2.4 36.1 1.0
O4 A:4WI401 2.6 35.6 1.0
O A:THR190 2.9 34.6 1.0
NE2 A:GLN192 3.3 36.2 1.0
N4 A:4WI401 3.6 35.4 1.0
O A:ARG188 3.6 32.1 1.0
CE A:MET165 3.7 35.1 1.0
H16 A:4WI401 3.9 35.4 0.0
C A:THR190 3.9 34.0 1.0
SD A:MET165 4.0 35.7 1.0
CD A:GLN192 4.0 37.7 1.0
N A:THR190 4.1 33.3 1.0
CG A:GLN192 4.4 34.3 1.0
CB A:GLN192 4.4 33.5 1.0
N A:GLN192 4.4 32.2 1.0
H25 A:4WI401 4.6 33.3 0.0
O A:GLU166 4.6 33.7 1.0
CD2 A:LEU167 4.6 38.0 1.0
CA A:THR190 4.7 33.9 1.0
CA A:GLN189 4.7 32.7 1.0
C A:ARG188 4.7 32.2 1.0
H15 A:4WI401 4.8 34.6 0.0
N A:ALA191 4.8 33.3 1.0
OE1 A:GLN192 4.8 40.0 1.0
C14 A:4WI401 4.8 34.6 1.0
C A:GLN189 4.9 32.9 1.0
CA A:ALA191 4.9 32.8 1.0
C A:ALA191 5.0 32.0 1.0

Fluorine binding site 3 out of 6 in 9auk

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Fluorine binding site 3 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.6
occ:1.00
 F3 A:4WI401 0.0 36.6 1.0
C22 A:4WI401 1.4 37.4 1.0
F2 A:4WI401 2.1 38.2 1.0
F1 A:4WI401 2.2 38.4 1.0
C21 A:4WI401 2.4 36.1 1.0
N4 A:4WI401 3.1 35.4 1.0
H16 A:4WI401 3.1 35.4 0.0
O4 A:4WI401 3.2 35.6 1.0
O A:GLU166 3.3 33.7 1.0
CD A:PRO168 3.4 39.4 1.0
CA A:LEU167 3.8 37.0 1.0
N A:PRO168 4.0 39.7 1.0
O A:THR190 4.0 34.6 1.0
CG A:PRO168 4.0 41.2 1.0
H17 A:4WI401 4.0 34.0 0.0
C A:LEU167 4.1 39.0 1.0
C A:GLU166 4.2 34.4 1.0
CD2 A:LEU167 4.3 38.0 1.0
N A:LEU167 4.4 35.8 1.0
C14 A:4WI401 4.5 34.6 1.0
N A:GLN192 4.5 32.2 1.0
H15 A:4WI401 4.7 34.6 0.0
H30 A:4WI401 4.7 33.3 0.0
C A:THR190 4.7 34.0 1.0
CB A:LEU167 4.8 36.6 1.0
CA A:ALA191 4.9 32.8 1.0
O A:GLN192 4.9 33.8 1.0
C16 A:4WI401 4.9 34.0 1.0
CE A:MET165 5.0 35.1 1.0
CA A:PRO168 5.0 40.3 1.0

Fluorine binding site 4 out of 6 in 9auk

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Fluorine binding site 4 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:35.7
occ:1.00
 F1 B:4WI401 0.0 35.7 1.0
C22 B:4WI401 1.4 35.7 1.0
F2 B:4WI401 2.2 37.3 1.0
F3 B:4WI401 2.2 35.5 1.0
H16 B:4WI401 2.4 33.3 0.0
C21 B:4WI401 2.4 34.6 1.0
N4 B:4WI401 2.7 33.3 1.0
O B:GLU166 2.9 31.5 1.0
O4 B:4WI401 3.4 34.3 1.0
C B:GLU166 3.4 31.8 1.0
CB B:MET165 3.5 26.7 1.0
CD2 B:LEU167 3.5 37.2 1.0
CE B:MET165 3.7 31.8 1.0
CA B:LEU167 3.8 35.2 1.0
N B:LEU167 3.8 33.5 1.0
SD B:MET165 3.8 34.4 1.0
N B:GLU166 4.0 28.5 1.0
C14 B:4WI401 4.1 32.2 1.0
CG B:MET165 4.3 28.8 1.0
O3 B:4WI401 4.3 32.7 1.0
CA B:GLU166 4.4 29.9 1.0
C13 B:4WI401 4.4 32.4 1.0
CG B:LEU167 4.5 36.8 1.0
H30 B:4WI401 4.5 30.3 0.0
C B:MET165 4.6 27.2 1.0
H15 B:4WI401 4.6 32.2 0.0
CA B:MET165 4.7 26.7 1.0
CB B:LEU167 4.7 35.2 1.0
CG2 B:VAL173 4.8 26.2 1.0
C B:LEU167 4.8 36.9 1.0
H17 B:4WI401 4.8 30.6 0.0
NE2 B:GLN192 4.8 27.4 1.0
H25 B:4WI401 4.8 31.2 0.0
O B:THR190 5.0 30.0 1.0
CD B:PRO168 5.0 37.9 1.0

Fluorine binding site 5 out of 6 in 9auk

Go back to Fluorine Binding Sites List in 9auk
Fluorine binding site 5 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:37.3
occ:1.00
 F2 B:4WI401 0.0 37.3 1.0
C22 B:4WI401 1.4 35.7 1.0
F3 B:4WI401 2.1 35.5 1.0
F1 B:4WI401 2.2 35.7 1.0
C21 B:4WI401 2.4 34.6 1.0
O4 B:4WI401 2.7 34.3 1.0
O B:THR190 2.9 30.0 1.0
NE2 B:GLN192 3.2 27.4 1.0
N4 B:4WI401 3.6 33.3 1.0
CD B:GLN192 3.8 30.3 1.0
H16 B:4WI401 3.8 33.3 0.0
O B:ARG188 3.8 31.0 1.0
CG B:GLN192 4.0 30.6 1.0
CE B:MET165 4.0 31.8 1.0
CB B:GLN192 4.0 31.3 1.0
SD B:MET165 4.1 34.4 1.0
C B:THR190 4.1 30.2 1.0
CD2 B:LEU167 4.3 37.2 1.0
N B:THR190 4.4 30.2 1.0
N B:GLN192 4.5 30.0 1.0
OE1 B:GLN192 4.6 31.7 1.0
O B:GLU166 4.7 31.5 1.0
H25 B:4WI401 4.8 31.2 0.0
H15 B:4WI401 4.8 32.2 0.0
C14 B:4WI401 4.8 32.2 1.0
CA B:GLN192 4.9 30.6 1.0
CA B:THR190 4.9 30.7 1.0
C B:ARG188 4.9 30.1 1.0

Fluorine binding site 6 out of 6 in 9auk

Go back to Fluorine Binding Sites List in 9auk
Fluorine binding site 6 out of 6 in the Structure of Sars-Cov-2 Mpro Mutant (A173V) 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 (A173V) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:35.5
occ:1.00
 F3 B:4WI401 0.0 35.5 1.0
C22 B:4WI401 1.4 35.7 1.0
F2 B:4WI401 2.1 37.3 1.0
F1 B:4WI401 2.2 35.7 1.0
C21 B:4WI401 2.4 34.6 1.0
N4 B:4WI401 3.0 33.3 1.0
H16 B:4WI401 3.0 33.3 0.0
O4 B:4WI401 3.2 34.3 1.0
O B:GLU166 3.3 31.5 1.0
CD B:PRO168 3.5 37.9 1.0
CA B:LEU167 3.7 35.2 1.0
H17 B:4WI401 3.8 30.6 0.0
O B:THR190 3.9 30.0 1.0
N B:PRO168 4.0 37.9 1.0
CD2 B:LEU167 4.1 37.2 1.0
C B:LEU167 4.1 36.9 1.0
CG B:PRO168 4.1 39.4 1.0
C B:GLU166 4.2 31.8 1.0
C14 B:4WI401 4.4 32.2 1.0
N B:LEU167 4.4 33.5 1.0
H30 B:4WI401 4.5 30.3 0.0
H15 B:4WI401 4.6 32.2 0.0
N B:GLN192 4.6 30.0 1.0
CB B:LEU167 4.7 35.2 1.0
C16 B:4WI401 4.7 30.6 1.0
C B:THR190 4.9 30.2 1.0
O B:GLN192 4.9 33.2 1.0
CB B:GLN192 4.9 31.3 1.0
H19 B:4WI401 5.0 30.6 0.0

Reference:

Y.Zhu, I.Yurgelonis, S.Noell, Q.Yang, S.Guan, Z.Li, L.Hao, H.Rothan, D.K.Rai, P.Mcmonagle, M.L.Baniecki, S.E.Greasley, O.Plotnikova, J.Lee, J.A.Nicki, R.Ferre, L.J.Byrnes, W.Liu, T.K.Craig, C.M.Steppan, P.Liberator, H.D.Soares, C.M.N.Allerton, A.S.Anderson, R.D.Cardin. In Vitro Selection and Analysis of Sars-Cov-2 Nirmatrelvir Resistance Mutations Contributing to Clinical Virus Resistance Surveillance. Sci Adv V. 10 L4013 2024.
ISSN: ESSN 2375-2548
PubMed: 39047088
DOI: 10.1126/SCIADV.ADL4013
Page generated: Sun Aug 11 11:22:57 2024

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