Fluorine in PDB 8h51: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h51 was solved by M.Lin, X.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.96 / 2.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.566, 63.394, 106.24, 90, 90, 90
R / Rfree (%) 18.8 / 23.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir (pdb code 8h51). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h51:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8h51

Go back to Fluorine Binding Sites List in 8h51
Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor 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 Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:46.0
occ:1.00
 F1 A:4WI401 0.0 46.0 1.0
C22 A:4WI401 1.4 41.0 1.0
F3 A:4WI401 2.2 44.7 1.0
F2 A:4WI401 2.2 50.6 1.0
C21 A:4WI401 2.4 33.9 1.0
O4 A:4WI401 3.0 39.9 1.0
N4 A:4WI401 3.4 28.2 1.0
O A:THR190 3.6 35.1 1.0
CD A:PRO168 3.7 41.2 1.0
N A:GLN192 4.0 35.9 1.0
C A:THR190 4.3 35.1 1.0
CA A:ALA191 4.3 33.2 1.0
O A:GLN192 4.3 36.9 1.0
CG A:PRO168 4.4 38.9 1.0
O A:VAL166 4.4 25.6 1.0
C14 A:4WI401 4.7 30.8 1.0
C A:ALA191 4.7 32.5 1.0
N A:ALA191 4.7 36.3 1.0
C17 A:4WI401 4.7 31.4 1.0
CA A:LEU167 4.7 35.5 1.0
CD2 A:LEU167 4.8 33.0 1.0
N A:PRO168 4.8 37.4 1.0
CA A:GLN192 5.0 36.3 1.0

Fluorine binding site 2 out of 3 in 8h51

Go back to Fluorine Binding Sites List in 8h51
Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor 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 Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.6
occ:1.00
 F2 A:4WI401 0.0 50.6 1.0
C22 A:4WI401 1.4 41.0 1.0
F3 A:4WI401 2.2 44.7 1.0
F1 A:4WI401 2.2 46.0 1.0
C21 A:4WI401 2.4 33.9 1.0
O A:VAL166 2.5 25.6 1.0
N4 A:4WI401 2.7 28.2 1.0
CA A:LEU167 3.2 35.5 1.0
CD2 A:LEU167 3.4 33.0 1.0
C A:VAL166 3.4 34.3 1.0
O4 A:4WI401 3.5 39.9 1.0
N A:LEU167 3.7 31.7 1.0
CE A:MET165 3.7 38.4 1.0
CD A:PRO168 3.8 41.2 1.0
CB A:LEU167 4.0 34.6 1.0
CG A:LEU167 4.0 38.2 1.0
C A:LEU167 4.1 38.8 1.0
C14 A:4WI401 4.1 30.8 1.0
N A:PRO168 4.4 37.4 1.0
O3 A:4WI401 4.6 34.3 1.0
C13 A:4WI401 4.7 31.9 1.0
CA A:VAL166 4.7 33.2 1.0
N A:VAL166 4.8 28.6 1.0
O A:GLN192 4.9 36.9 1.0

Fluorine binding site 3 out of 3 in 8h51

Go back to Fluorine Binding Sites List in 8h51
Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor 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 Sars-Cov-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.7
occ:1.00
 F3 A:4WI401 0.0 44.7 1.0
C22 A:4WI401 1.4 41.0 1.0
F2 A:4WI401 2.2 50.6 1.0
F1 A:4WI401 2.2 46.0 1.0
C21 A:4WI401 2.4 33.9 1.0
O4 A:4WI401 2.8 39.9 1.0
O A:THR190 3.0 35.1 1.0
CE A:MET165 3.1 38.4 1.0
NE2 A:GLN192 3.4 32.7 1.0
N4 A:4WI401 3.6 28.2 1.0
CD2 A:LEU167 3.9 33.0 1.0
CD A:GLN192 3.9 33.9 1.0
CB A:GLN192 4.0 30.2 1.0
CG A:GLN192 4.0 37.7 1.0
N A:GLN192 4.1 35.9 1.0
O A:ARG188 4.1 32.6 1.0
C A:THR190 4.1 35.1 1.0
N A:THR190 4.4 32.4 1.0
O A:VAL166 4.6 25.6 1.0
CA A:GLN192 4.6 36.3 1.0
C14 A:4WI401 4.7 30.8 1.0
O A:GLN192 4.8 36.9 1.0
OE1 A:GLN192 4.8 33.7 1.0
C A:ALA191 4.8 32.5 1.0
SD A:MET165 4.9 41.7 1.0
CA A:ALA191 5.0 33.2 1.0
CD A:PRO168 5.0 41.2 1.0
CA A:THR190 5.0 35.7 1.0

Reference:

Y.Duan, H.Zhou, X.Liu, S.Iketani, M.Lin, X.Zhang, Q.Bian, H.Wang, H.Sun, S.J.Hong, B.Culbertson, H.Mohri, M.I.Luck, Y.Zhu, X.Liu, Y.Lu, X.Yang, K.Yang, Y.Sabo, A.Chavez, S.P.Goff, Z.Rao, D.D.Ho, H.Yang. Molecular Mechanisms of Sars-Cov-2 Resistance to Nirmatrelvir. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37696289
DOI: 10.1038/S41586-023-06609-0
Page generated: Fri Aug 2 20:00:47 2024

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