Fluorine in PDB 7vlq: Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121

Enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121

All present enzymatic activity of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121, PDB code: 7vlq was solved by X.L.Zhou, F.L.Zhong, C.Lin, J.Zhang, J.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.64 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.854, 102.016, 103.27, 90, 90, 90
R / Rfree (%) 20 / 22.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121 (pdb code 7vlq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121, PDB code: 7vlq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


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 in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:32.3
occ:1.00
 F1 A:4WI401 0.0 32.3 1.0
C22 A:4WI401 1.3 30.5 1.0
F2 A:4WI401 2.2 33.1 1.0
F3 A:4WI401 2.2 31.0 1.0
C21 A:4WI401 2.3 27.0 1.0
O4 A:4WI401 2.6 28.9 1.0
CG A:GLN192 3.1 31.7 1.0
O A:THR190 3.3 29.9 1.0
CE A:MET165 3.3 30.2 1.0
NE2 A:GLN192 3.4 25.1 1.0
N4 A:4WI401 3.5 24.8 1.0
CD A:GLN192 3.7 30.4 1.0
O A:ARG188 4.1 19.1 1.0
N A:GLN192 4.4 25.8 1.0
CD2 A:LEU167 4.4 28.4 1.0
CB A:GLN192 4.4 29.7 1.0
C A:THR190 4.4 28.4 1.0
N A:THR190 4.5 27.2 1.0
O A:GLU166 4.6 21.5 1.0
O A:GLN192 4.7 26.5 1.0
C14 A:4WI401 4.7 24.4 1.0
OE1 A:GLN192 4.8 23.8 1.0
CA A:GLN192 4.8 26.6 1.0
CA A:GLN189 4.9 21.4 1.0
SD A:MET165 5.0 32.6 1.0

Fluorine binding site 2 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


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 in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.1
occ:1.00
 F2 A:4WI401 0.0 33.1 1.0
C22 A:4WI401 1.3 30.5 1.0
F1 A:4WI401 2.2 32.3 1.0
F3 A:4WI401 2.2 31.0 1.0
C21 A:4WI401 2.3 27.0 1.0
N4 A:4WI401 2.7 24.8 1.0
O A:GLU166 2.8 21.5 1.0
CE A:MET165 2.9 30.2 1.0
O4 A:4WI401 3.3 28.9 1.0
C A:GLU166 3.5 24.6 1.0
CD2 A:LEU167 3.6 28.4 1.0
CA A:LEU167 3.8 22.3 1.0
N A:LEU167 3.9 20.7 1.0
CG A:MET165 3.9 24.3 1.0
CG A:LEU167 4.0 27.2 1.0
CB A:MET165 4.0 16.9 1.0
SD A:MET165 4.1 32.6 1.0
C14 A:4WI401 4.1 24.4 1.0
N A:GLU166 4.2 19.3 1.0
O A:HOH558 4.3 25.6 1.0
O3 A:4WI401 4.4 20.3 1.0
C13 A:4WI401 4.5 25.0 1.0
CG A:GLN192 4.5 31.7 1.0
CB A:LEU167 4.5 21.3 1.0
CA A:GLU166 4.5 20.9 1.0
NE2 A:GLN192 4.6 25.1 1.0
C A:MET165 4.8 21.0 1.0
CD A:GLN192 4.8 30.4 1.0
C A:LEU167 4.9 26.4 1.0
CD A:PRO168 5.0 29.3 1.0

Fluorine binding site 3 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


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 in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:31.0
occ:1.00
 F3 A:4WI401 0.0 31.0 1.0
C22 A:4WI401 1.3 30.5 1.0
F2 A:4WI401 2.2 33.1 1.0
F1 A:4WI401 2.2 32.3 1.0
C21 A:4WI401 2.3 27.0 1.0
N4 A:4WI401 2.9 24.8 1.0
O A:HOH558 2.9 25.6 1.0
O A:GLU166 3.1 21.5 1.0
O4 A:4WI401 3.2 28.9 1.0
CD A:PRO168 3.6 29.3 1.0
CA A:LEU167 3.7 22.3 1.0
C A:GLU166 4.1 24.6 1.0
N A:PRO168 4.2 27.3 1.0
C A:LEU167 4.2 26.4 1.0
CD2 A:LEU167 4.2 28.4 1.0
C14 A:4WI401 4.3 24.4 1.0
N A:LEU167 4.3 20.7 1.0
O A:GLN192 4.4 26.5 1.0
C16 A:4WI401 4.4 25.7 1.0
CB A:LEU167 4.7 21.3 1.0
CG A:GLN192 4.7 31.7 1.0
CG A:LEU167 4.8 27.2 1.0
CG A:PRO168 4.8 36.4 1.0
CE A:MET165 4.8 30.2 1.0
O A:THR190 4.8 29.9 1.0
C15 A:4WI401 4.9 27.0 1.0

Fluorine binding site 4 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.3
occ:1.00
 F1 B:4WI401 0.0 33.3 1.0
C22 B:4WI401 1.4 33.9 1.0
F3 B:4WI401 2.0 33.6 1.0
F2 B:4WI401 2.0 31.5 1.0
C21 B:4WI401 2.3 29.3 1.0
O4 B:4WI401 2.5 32.1 1.0
CG B:GLN192 2.9 31.6 1.0
O B:THR190 3.0 29.4 1.0
NE2 B:GLN192 3.1 29.2 1.0
CD B:GLN192 3.5 30.4 1.0
N4 B:4WI401 3.5 25.5 1.0
CE B:MET165 3.5 29.9 1.0
N B:GLN192 4.2 22.9 1.0
C B:THR190 4.2 36.9 1.0
CB B:GLN192 4.2 30.5 1.0
O B:ARG188 4.3 26.3 1.0
CD2 B:LEU167 4.4 26.4 1.0
N B:THR190 4.4 33.5 1.0
OE1 B:GLN192 4.6 22.7 1.0
O B:GLN192 4.7 24.1 1.0
O B:GLU166 4.7 24.2 1.0
C14 B:4WI401 4.7 25.0 1.0
CA B:GLN192 4.7 25.9 1.0
C B:ALA191 4.9 28.2 1.0
C B:GLN192 5.0 25.7 1.0

Fluorine binding site 5 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:31.5
occ:1.00
 F2 B:4WI401 0.0 31.5 1.0
C22 B:4WI401 1.1 33.9 1.0
F3 B:4WI401 1.9 33.6 1.0
F1 B:4WI401 2.0 33.3 1.0
C21 B:4WI401 2.3 29.3 1.0
N4 B:4WI401 2.9 25.5 1.0
O4 B:4WI401 3.1 32.1 1.0
O B:HOH528 3.3 31.0 1.0
O B:GLU166 3.3 24.2 1.0
CA B:LEU167 3.8 23.9 1.0
CD B:PRO168 3.8 28.1 1.0
O B:GLN192 4.2 24.1 1.0
CD2 B:LEU167 4.2 26.4 1.0
C B:GLU166 4.2 23.4 1.0
CG B:GLN192 4.2 31.6 1.0
O B:THR190 4.3 29.4 1.0
C14 B:4WI401 4.3 25.0 1.0
N B:PRO168 4.4 25.7 1.0
C B:LEU167 4.4 29.2 1.0
N B:LEU167 4.4 23.9 1.0
CE B:MET165 4.6 29.9 1.0
N B:GLN192 4.6 22.9 1.0
C16 B:4WI401 4.7 24.9 1.0
CB B:LEU167 4.7 22.8 1.0
CG B:LEU167 4.8 25.3 1.0
C B:GLN192 4.9 25.7 1.0
CG B:PRO168 4.9 32.6 1.0

Fluorine binding site 6 out of 6 in 7vlq

Go back to Fluorine Binding Sites List in 7vlq
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P212121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:33.6
occ:1.00
 F3 B:4WI401 0.0 33.6 1.0
C22 B:4WI401 1.1 33.9 1.0
F2 B:4WI401 1.9 31.5 1.0
F1 B:4WI401 2.0 33.3 1.0
C21 B:4WI401 2.2 29.3 1.0
N4 B:4WI401 2.7 25.5 1.0
O B:GLU166 2.9 24.2 1.0
CE B:MET165 2.9 29.9 1.0
O4 B:4WI401 3.1 32.1 1.0
C B:GLU166 3.6 23.4 1.0
CD2 B:LEU167 3.6 26.4 1.0
CA B:LEU167 3.8 23.9 1.0
N B:LEU167 4.0 23.9 1.0
C14 B:4WI401 4.1 25.0 1.0
CG B:LEU167 4.1 25.3 1.0
CG B:GLN192 4.1 31.6 1.0
CB B:MET165 4.2 18.2 1.0
NE2 B:GLN192 4.3 29.2 1.0
O B:HOH528 4.3 31.0 1.0
N B:GLU166 4.4 21.1 1.0
SD B:MET165 4.4 30.0 1.0
O3 B:4WI401 4.5 23.3 1.0
C13 B:4WI401 4.5 23.7 1.0
CG B:MET165 4.5 21.4 1.0
CB B:LEU167 4.5 22.8 1.0
CD B:GLN192 4.6 30.4 1.0
CA B:GLU166 4.6 23.0 1.0
C B:LEU167 4.9 29.2 1.0
CD B:PRO168 5.0 28.1 1.0
O B:THR190 5.0 29.4 1.0

Reference:

J.Li, C.Lin, X.Zhou, F.Zhong, P.Zeng, Y.Yang, Y.Zhang, B.Yu, X.Fan, P.J.Mccormick, R.Fu, Y.Fu, H.Jiang, J.Zhang. Structural Basis of the Main Proteases of Coronavirus Bound to Drug Candidate Pf-07321332. J.Virol. V. 96 01321 2022.
ISSN: ESSN 1098-5514
PubMed: 35389231
DOI: 10.1128/JVI.02013-21
Page generated: Fri Aug 2 14:30:18 2024

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