Fluorine in PDB 9aum: Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

The structure of Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 9aum 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)	27.29 / 1.54
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.396, 63.855, 105.163, 90, 90, 90
R / Rfree (%)	19.5 / 22.9

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332) (pdb code 9aum). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 9aum:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) 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 (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.7 occ:1.00 F1 A:4WI401 0.0 26.7 1.0 C22 A:4WI401 1.3 25.6 1.0 F3 A:4WI401 2.1 27.6 1.0 F2 A:4WI401 2.2 27.0 1.0 H16 A:4WI401 2.3 16.8 0.0 C21 A:4WI401 2.4 21.7 1.0 N4 A:4WI401 2.7 16.8 1.0 CE A:MET165 2.8 26.4 1.0 O A:GLU166 2.9 14.1 1.0 CD2 A:LEU167 3.4 17.9 1.0 O4 A:4WI401 3.4 22.4 1.0 C A:GLU166 3.6 14.3 1.0 CG A:MET165 4.0 15.5 1.0 SD A:MET165 4.0 27.0 1.0 CB A:MET165 4.0 14.0 1.0 CA A:LEU167 4.0 16.9 1.0 N A:LEU167 4.0 14.8 1.0 CG A:LEU167 4.1 17.2 1.0 C14 A:4WI401 4.1 14.5 1.0 N A:GLU166 4.2 12.7 1.0 O3 A:4WI401 4.4 13.1 1.0 C13 A:4WI401 4.4 13.8 1.0 NE2 A:GLN192 4.5 17.5 1.0 H25 A:4WI401 4.5 15.3 0.0 H30 A:4WI401 4.6 14.2 0.0 H15 A:4WI401 4.6 14.5 0.0 CA A:GLU166 4.6 13.3 1.0 O A:HOH713 4.6 47.5 1.0 CB A:LEU167 4.6 16.4 1.0 H17 A:4WI401 4.8 15.2 0.0 C A:MET165 4.8 13.8 1.0 CB A:GLN192 4.8 21.6 1.0 CD A:GLN192 5.0 20.9 1.0

Fluorine binding site 2 out of 3 in the Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) 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 (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.0 occ:1.00 F2 A:4WI401 0.0 27.0 1.0 C22 A:4WI401 1.4 25.6 1.0 F1 A:4WI401 2.2 26.7 1.0 F3 A:4WI401 2.2 27.6 1.0 C21 A:4WI401 2.3 21.7 1.0 O4 A:4WI401 2.7 22.4 1.0 O A:THR190 2.9 25.8 1.0 NE2 A:GLN192 3.1 17.5 1.0 CE A:MET165 3.4 26.4 1.0 N4 A:4WI401 3.5 16.8 1.0 CB A:GLN192 3.7 21.6 1.0 CD A:GLN192 3.7 20.9 1.0 H16 A:4WI401 3.8 16.8 0.0 CG A:GLN192 3.8 20.3 1.0 O A:ARG188 3.9 15.6 1.0 C A:THR190 4.1 25.8 1.0 N A:GLN192 4.1 23.3 1.0 O A:HOH639 4.3 43.1 1.0 CD2 A:LEU167 4.3 17.9 1.0 N A:THR190 4.3 21.3 1.0 CA A:GLN192 4.5 21.9 1.0 O A:HOH781 4.7 46.5 1.0 O A:GLU166 4.7 14.1 1.0 OE1 A:GLN192 4.7 21.5 1.0 H25 A:4WI401 4.7 15.3 0.0 H15 A:4WI401 4.7 14.5 0.0 C14 A:4WI401 4.8 14.5 1.0 O A:GLN192 4.8 22.6 1.0 C A:ALA191 4.8 25.0 1.0 CA A:THR190 4.9 24.6 1.0 SD A:MET165 4.9 27.0 1.0 N A:ALA191 5.0 26.4 1.0 CA A:GLN189 5.0 17.3 1.0

Fluorine binding site 3 out of 3 in the Structure of Sars-Cov-2 Mpro Mutant (T21I,S144A,T304I) 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 (T21I,S144A,T304I) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.6 occ:1.00 F3 A:4WI401 0.0 27.6 1.0 C22 A:4WI401 1.3 25.6 1.0 F1 A:4WI401 2.1 26.7 1.0 F2 A:4WI401 2.2 27.0 1.0 C21 A:4WI401 2.4 21.7 1.0 H16 A:4WI401 2.9 16.8 0.0 N4 A:4WI401 2.9 16.8 1.0 O4 A:4WI401 3.2 22.4 1.0 O A:GLU166 3.2 14.1 1.0 O A:HOH713 3.2 47.5 1.0 O A:HOH639 3.2 43.1 1.0 O A:HOH781 3.6 46.5 1.0 H17 A:4WI401 3.8 15.2 0.0 CA A:LEU167 3.9 16.9 1.0 CD2 A:LEU167 3.9 17.9 1.0 CD A:PRO168 4.1 24.8 1.0 C A:GLU166 4.2 14.3 1.0 O A:GLN192 4.2 22.6 1.0 C14 A:4WI401 4.3 14.5 1.0 O A:THR190 4.4 25.8 1.0 H30 A:4WI401 4.4 14.2 0.0 N A:LEU167 4.4 14.8 1.0 N A:GLN192 4.5 23.3 1.0 C A:LEU167 4.6 21.3 1.0 H15 A:4WI401 4.6 14.5 0.0 N A:PRO168 4.7 24.6 1.0 CB A:GLN192 4.7 21.6 1.0 C16 A:4WI401 4.7 15.2 1.0 CE A:MET165 4.7 26.4 1.0 CG A:LEU167 4.7 17.2 1.0 CB A:LEU167 4.8 16.4 1.0 H19 A:4WI401 4.9 15.2 0.0 CG A:PRO168 4.9 27.2 1.0 C A:GLN192 5.0 22.6 1.0 CA A:GLN192 5.0 21.9 1.0

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