Atomistry » Fluorine » PDB 8h3g-8huo » 8h5p
Atomistry »
  Fluorine »
    PDB 8h3g-8huo »
      8h5p »

Fluorine in PDB 8h5p: Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F 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 (L50F and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5p 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) 27.90 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 45.65, 63.81, 105.761, 90, 90, 90
R / Rfree (%) 18 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Nirmatrelvir (pdb code 8h5p). 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 (L50F and E166V) in Complex with Inhibitor Nirmatrelvir, PDB code: 8h5p:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 1 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F 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 (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:36.0
occ:1.00
 F1 A:4WI401 0.0 36.0 1.0
C22 A:4WI401 1.4 33.7 1.0
F2 A:4WI401 2.2 34.1 1.0
F3 A:4WI401 2.3 35.5 1.0
C21 A:4WI401 2.4 29.7 1.0
N4 A:4WI401 3.1 24.1 1.0
O A:HOH648 3.2 36.9 1.0
O A:HOH658 3.2 41.8 1.0
O4 A:4WI401 3.2 29.9 1.0
O A:VAL166 3.5 23.1 1.0
CD A:PRO168 3.6 30.6 1.0
CA A:LEU167 3.9 26.3 1.0
CD2 A:LEU167 4.1 29.4 1.0
O A:GLN192 4.2 33.2 1.0
O A:THR190 4.3 33.7 1.0
N A:PRO168 4.3 30.7 1.0
C A:VAL166 4.4 23.8 1.0
CG A:PRO168 4.4 33.8 1.0
C A:LEU167 4.4 29.7 1.0
C14 A:4WI401 4.5 25.7 1.0
N A:LEU167 4.6 24.0 1.0
C16 A:4WI401 4.7 27.0 1.0
N A:GLN192 4.7 34.9 1.0
CB A:LEU167 4.8 27.5 1.0
CB A:GLN192 4.8 29.1 1.0
CE A:MET165 4.9 35.1 1.0
CG A:LEU167 4.9 24.4 1.0

Fluorine binding site 2 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 2 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F 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 (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.1
occ:1.00
 F2 A:4WI401 0.0 34.1 1.0
C22 A:4WI401 1.4 33.7 1.0
F1 A:4WI401 2.2 36.0 1.0
F3 A:4WI401 2.2 35.5 1.0
C21 A:4WI401 2.3 29.7 1.0
N4 A:4WI401 2.8 24.1 1.0
O A:VAL166 2.8 23.1 1.0
CE A:MET165 3.0 35.1 1.0
O4 A:4WI401 3.4 29.9 1.0
CD2 A:LEU167 3.4 29.4 1.0
C A:VAL166 3.5 23.8 1.0
CA A:LEU167 3.8 26.3 1.0
CG A:MET165 3.8 25.9 1.0
N A:LEU167 3.9 24.0 1.0
CB A:MET165 4.0 24.8 1.0
CG A:LEU167 4.0 24.4 1.0
C14 A:4WI401 4.1 25.7 1.0
SD A:MET165 4.2 34.6 1.0
O A:HOH648 4.3 36.9 1.0
O3 A:4WI401 4.4 24.1 1.0
N A:VAL166 4.4 21.8 1.0
C13 A:4WI401 4.4 25.7 1.0
CB A:LEU167 4.4 27.5 1.0
CA A:VAL166 4.6 22.5 1.0
NE2 A:GLN192 4.7 27.4 1.0
CD A:PRO168 4.9 30.6 1.0
C A:LEU167 4.9 29.7 1.0
CB A:GLN192 5.0 29.1 1.0

Fluorine binding site 3 out of 3 in 8h5p

Go back to Fluorine Binding Sites List in 8h5p
Fluorine binding site 3 out of 3 in the Crystal Structure of Sars-Cov-2 Main Protease (Mpro) Double Mutant (L50F 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 (L50F and E166V) in Complex with Inhibitor Nirmatrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:1.00
 F3 A:4WI401 0.0 35.5 1.0
C22 A:4WI401 1.4 33.7 1.0
F2 A:4WI401 2.2 34.1 1.0
F1 A:4WI401 2.3 36.0 1.0
C21 A:4WI401 2.4 29.7 1.0
O4 A:4WI401 2.7 29.9 1.0
O A:THR190 3.0 33.7 1.0
NE2 A:GLN192 3.2 27.4 1.0
CE A:MET165 3.3 35.1 1.0
N4 A:4WI401 3.7 24.1 1.0
CB A:GLN192 3.7 29.1 1.0
CD A:GLN192 3.7 29.8 1.0
CG A:GLN192 3.7 31.1 1.0
O A:ARG188 4.0 27.8 1.0
C A:THR190 4.2 36.8 1.0
O A:HOH658 4.2 41.8 1.0
N A:GLN192 4.2 34.9 1.0
CD2 A:LEU167 4.2 29.4 1.0
N A:THR190 4.3 31.2 1.0
CA A:GLN192 4.5 28.9 1.0
OE1 A:GLN192 4.7 27.0 1.0
O A:GLN192 4.7 33.2 1.0
O A:VAL166 4.8 23.1 1.0
C14 A:4WI401 4.8 25.7 1.0
CA A:THR190 4.9 35.9 1.0
C A:ALA191 5.0 35.4 1.0
C A:GLN192 5.0 30.9 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: Thu Dec 28 04:34:21 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy