Fluorine in PDB 7u28: Structure of Sars-Cov-2 Mpro Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332)

Enzymatic activity of Structure of Sars-Cov-2 Mpro Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332)

All present enzymatic activity of Structure of Sars-Cov-2 Mpro Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332):
3.4.22.69;

Protein crystallography data

The structure of Structure of Sars-Cov-2 Mpro Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7u28 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) 112.33 / 1.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.551, 53.795, 114.891, 90, 102.13, 90
R / Rfree (%) 20.8 / 24.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Sars-Cov-2 Mpro Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) (pdb code 7u28). 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332), PDB code: 7u28:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 1 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.8
occ:1.00
 F1 A:4WI401 0.0 30.8 1.0
C22 A:4WI401 1.4 30.1 1.0
F2 A:4WI401 2.2 30.7 1.0
F3 A:4WI401 2.2 31.1 1.0
C21 A:4WI401 2.4 27.6 1.0
N4 A:4WI401 2.8 24.4 1.0
O A:GLU166 2.9 22.3 1.0
CE A:MET165 3.0 32.4 1.0
O4 A:4WI401 3.5 28.1 1.0
C A:GLU166 3.5 22.6 1.0
CD2 A:LEU167 3.6 31.0 1.0
SD A:MET165 3.8 31.0 1.0
CB A:MET165 3.8 19.1 1.0
CG A:MET165 3.9 23.3 1.0
CA A:LEU167 3.9 27.6 1.0
N A:LEU167 3.9 24.9 1.0
C14 A:4WI401 4.1 22.6 1.0
N A:GLU166 4.2 18.9 1.0
CG A:LEU167 4.2 30.2 1.0
O3 A:4WI401 4.2 22.1 1.0
C13 A:4WI401 4.3 22.5 1.0
NE2 A:GLN192 4.4 22.9 1.0
CA A:GLU166 4.5 20.4 1.0
O A:HOH612 4.5 45.0 1.0
CB A:LEU167 4.7 28.0 1.0
C A:MET165 4.7 18.4 1.0
CA A:MET165 4.9 17.6 1.0
CD A:PRO168 4.9 33.2 1.0
C A:LEU167 5.0 30.6 1.0
O A:THR190 5.0 24.6 1.0

Fluorine binding site 2 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 2 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.7
occ:1.00
 F2 A:4WI401 0.0 30.7 1.0
C22 A:4WI401 1.4 30.1 1.0
F1 A:4WI401 2.2 30.8 1.0
F3 A:4WI401 2.2 31.1 1.0
C21 A:4WI401 2.4 27.6 1.0
O4 A:4WI401 2.7 28.1 1.0
O A:THR190 2.9 24.6 1.0
NE2 A:GLN192 3.0 22.9 1.0
N4 A:4WI401 3.6 24.4 1.0
O A:ARG188 3.6 18.2 1.0
CD A:GLN192 3.7 24.3 1.0
CE A:MET165 3.8 32.4 1.0
C A:THR190 4.0 24.5 1.0
CG A:GLN192 4.0 23.6 1.0
CB A:GLN192 4.1 23.2 1.0
N A:THR190 4.1 22.5 1.0
N A:GLN192 4.4 23.5 1.0
CD2 A:LEU167 4.5 31.0 1.0
SD A:MET165 4.6 31.0 1.0
OE1 A:GLN192 4.6 24.4 1.0
O A:GLU166 4.7 22.3 1.0
C A:ARG188 4.7 17.8 1.0
CA A:THR190 4.8 24.1 1.0
C14 A:4WI401 4.8 22.6 1.0
CA A:GLN189 4.8 19.8 1.0
C A:ALA191 4.9 24.1 1.0
N A:ALA191 4.9 24.4 1.0
CA A:GLN192 4.9 23.7 1.0
CA A:ALA191 5.0 24.7 1.0
C A:GLN189 5.0 22.1 1.0

Fluorine binding site 3 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 3 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:31.1
occ:1.00
 F3 A:4WI401 0.0 31.1 1.0
C22 A:4WI401 1.4 30.1 1.0
F1 A:4WI401 2.2 30.8 1.0
F2 A:4WI401 2.2 30.7 1.0
C21 A:4WI401 2.3 27.6 1.0
N4 A:4WI401 3.0 24.4 1.0
O A:HOH612 3.0 45.0 1.0
O4 A:4WI401 3.1 28.1 1.0
O A:GLU166 3.2 22.3 1.0
CD A:PRO168 3.4 33.2 1.0
CA A:LEU167 3.7 27.6 1.0
N A:PRO168 4.0 32.9 1.0
O A:THR190 4.0 24.6 1.0
CG A:PRO168 4.0 35.5 1.0
CD2 A:LEU167 4.1 31.0 1.0
C A:GLU166 4.1 22.6 1.0
C A:LEU167 4.1 30.6 1.0
N A:LEU167 4.3 24.9 1.0
C14 A:4WI401 4.4 22.6 1.0
N A:GLN192 4.6 23.5 1.0
CB A:LEU167 4.7 28.0 1.0
CG A:LEU167 4.9 30.2 1.0
CE A:MET165 4.9 32.4 1.0
C16 A:4WI401 4.9 21.2 1.0
CB A:GLN192 4.9 23.2 1.0
C A:THR190 4.9 24.5 1.0
CA A:PRO168 5.0 34.5 1.0

Fluorine binding site 4 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 4 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:32.1
occ:1.00
 F1 B:4WI401 0.0 32.1 1.0
C22 B:4WI401 1.4 31.7 1.0
F2 B:4WI401 2.2 32.5 1.0
F3 B:4WI401 2.2 32.9 1.0
C21 B:4WI401 2.4 29.6 1.0
N4 B:4WI401 2.8 26.6 1.0
O B:GLU166 2.8 21.9 1.0
CE B:MET165 2.8 28.8 1.0
C B:GLU166 3.4 22.2 1.0
CD2 B:LEU167 3.4 30.0 1.0
O4 B:4WI401 3.4 30.4 1.0
CA B:LEU167 3.7 26.0 1.0
CG B:MET165 3.8 21.5 1.0
N B:LEU167 3.8 23.9 1.0
SD B:MET165 3.9 29.8 1.0
CB B:MET165 4.0 18.9 1.0
O B:HOH618 4.0 37.9 1.0
N B:GLU166 4.1 19.6 1.0
C14 B:4WI401 4.1 24.2 1.0
O3 B:4WI401 4.3 22.5 1.0
CG B:LEU167 4.3 29.4 1.0
C13 B:4WI401 4.4 23.0 1.0
CA B:GLU166 4.4 20.4 1.0
NE2 B:GLN192 4.5 22.8 1.0
CB B:LEU167 4.6 27.0 1.0
C B:MET165 4.7 18.6 1.0
C B:LEU167 4.8 27.9 1.0
CD B:PRO168 4.9 28.6 1.0
O B:THR190 5.0 23.7 1.0
CA B:MET165 5.0 17.6 1.0

Fluorine binding site 5 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 5 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:32.5
occ:1.00
 F2 B:4WI401 0.0 32.5 1.0
C22 B:4WI401 1.4 31.7 1.0
F1 B:4WI401 2.2 32.1 1.0
F3 B:4WI401 2.2 32.9 1.0
C21 B:4WI401 2.4 29.6 1.0
O4 B:4WI401 2.6 30.4 1.0
CE B:MET165 2.9 28.8 1.0
NE2 B:GLN192 2.9 22.8 1.0
O B:THR190 3.0 23.7 1.0
O B:ARG188 3.5 16.4 1.0
N4 B:4WI401 3.6 26.6 1.0
CD B:GLN192 3.7 23.2 1.0
C B:THR190 4.0 23.3 1.0
CG B:GLN192 4.1 21.5 1.0
N B:THR190 4.1 20.7 1.0
CB B:GLN192 4.3 21.7 1.0
CD2 B:LEU167 4.4 30.0 1.0
SD B:MET165 4.4 29.8 1.0
N B:GLN192 4.5 22.0 1.0
OE1 B:GLN192 4.6 23.9 1.0
C B:ARG188 4.7 17.0 1.0
O B:GLU166 4.7 21.9 1.0
CA B:THR190 4.7 22.2 1.0
CA B:GLN189 4.8 17.6 1.0
C14 B:4WI401 4.8 24.2 1.0
O B:HOH618 4.9 37.9 1.0
O B:VAL186 4.9 17.0 1.0
N B:ALA191 4.9 23.6 1.0
C B:GLN189 4.9 19.5 1.0
CA B:ALA191 4.9 24.2 1.0
C B:ALA191 5.0 22.8 1.0

Fluorine binding site 6 out of 6 in 7u28

Go back to Fluorine Binding Sites List in 7u28
Fluorine binding site 6 out of 6 in the Structure of Sars-Cov-2 Mpro Lambda (G15S) 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 Lambda (G15S) in Complex with Nirmatrelvir (Pf-07321332) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:32.9
occ:1.00
 F3 B:4WI401 0.0 32.9 1.0
C22 B:4WI401 1.4 31.7 1.0
F2 B:4WI401 2.2 32.5 1.0
F1 B:4WI401 2.2 32.1 1.0
C21 B:4WI401 2.4 29.6 1.0
O B:HOH618 2.8 37.9 1.0
N4 B:4WI401 3.1 26.6 1.0
O4 B:4WI401 3.1 30.4 1.0
O B:GLU166 3.5 21.9 1.0
CD B:PRO168 3.5 28.6 1.0
O B:THR190 3.8 23.7 1.0
CA B:LEU167 3.9 26.0 1.0
CG B:PRO168 4.1 30.4 1.0
N B:PRO168 4.1 28.9 1.0
CD2 B:LEU167 4.2 30.0 1.0
C B:LEU167 4.3 27.9 1.0
N B:GLN192 4.3 22.0 1.0
C B:GLU166 4.4 22.2 1.0
C14 B:4WI401 4.4 24.2 1.0
CE B:MET165 4.5 28.8 1.0
CA B:ALA191 4.5 24.2 1.0
C B:THR190 4.5 23.3 1.0
N B:LEU167 4.6 23.9 1.0
NE2 B:GLN192 4.8 22.8 1.0
CB B:LEU167 4.8 27.0 1.0
C16 B:4WI401 4.9 23.6 1.0
N B:ALA191 4.9 23.6 1.0
C B:ALA191 4.9 22.8 1.0
CB B:GLN192 4.9 21.7 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 13:50:32 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy