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Fluorine in PDB 7vlp: Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211, PDB code: 7vlp was solved by X.L.Zhou, F.L.Zhong, C.Lin, J.Li, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.43 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.484, 98.695, 59.423, 90, 108.72, 90
R / Rfree (%) 19.5 / 21.9

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 P1211 (pdb code 7vlp). 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 P1211, PDB code: 7vlp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.6
occ:1.00
F1 A:4WI401 0.0 30.6 1.0
C22 A:4WI401 1.2 27.1 1.0
F3 A:4WI401 2.0 29.6 1.0
F2 A:4WI401 2.1 27.6 1.0
C21 A:4WI401 2.3 24.3 1.0
N4 A:4WI401 2.9 20.8 1.0
O A:HOH564 3.1 26.6 1.0
O4 A:4WI401 3.2 26.8 1.0
O A:GLU166 3.2 19.3 1.0
CD A:PRO168 3.6 27.5 1.0
CA A:LEU167 3.9 21.3 1.0
C A:GLU166 4.2 20.1 1.0
CD2 A:LEU167 4.2 25.3 1.0
N A:PRO168 4.2 24.5 1.0
C14 A:4WI401 4.3 19.7 1.0
O A:GLN192 4.3 24.8 1.0
C A:LEU167 4.3 22.9 1.0
O A:THR190 4.4 25.5 1.0
N A:LEU167 4.4 19.2 1.0
C16 A:4WI401 4.6 22.0 1.0
CG A:PRO168 4.6 28.8 1.0
N A:GLN192 4.7 24.0 1.0
CE A:MET165 4.8 27.2 1.0
CB A:GLN192 4.8 22.3 1.0
CB A:LEU167 4.9 21.4 1.0
C15 A:4WI401 4.9 20.3 1.0
CG A:LEU167 4.9 23.6 1.0

Fluorine binding site 2 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.6
occ:1.00
F2 A:4WI401 0.0 27.6 1.0
C22 A:4WI401 1.3 27.1 1.0
F3 A:4WI401 2.1 29.6 1.0
F1 A:4WI401 2.1 30.6 1.0
C21 A:4WI401 2.3 24.3 1.0
O4 A:4WI401 2.6 26.8 1.0
O A:THR190 3.0 25.5 1.0
N4 A:4WI401 3.5 20.8 1.0
NE2 A:GLN192 3.5 22.3 1.0
CE A:MET165 3.6 27.2 1.0
CB A:GLN192 3.7 22.3 1.0
CG A:GLN192 4.0 24.4 1.0
CD A:GLN192 4.0 20.8 1.0
N A:GLN192 4.0 24.0 1.0
C A:THR190 4.2 23.9 1.0
O A:ARG188 4.3 21.4 1.0
CA A:GLN192 4.4 21.9 1.0
N A:THR190 4.4 21.6 1.0
CD2 A:LEU167 4.4 25.3 1.0
O A:GLN192 4.6 24.8 1.0
O A:GLU166 4.7 19.3 1.0
C14 A:4WI401 4.7 19.7 1.0
C A:ALA191 4.7 25.1 1.0
C A:GLN192 4.9 22.2 1.0
OE1 A:GLN192 4.9 20.9 1.0

Fluorine binding site 3 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.6
occ:1.00
F3 A:4WI401 0.0 29.6 1.0
C22 A:4WI401 1.3 27.1 1.0
F1 A:4WI401 2.0 30.6 1.0
F2 A:4WI401 2.1 27.6 1.0
C21 A:4WI401 2.3 24.3 1.0
N4 A:4WI401 2.8 20.8 1.0
O A:GLU166 2.9 19.3 1.0
CE A:MET165 3.0 27.2 1.0
O4 A:4WI401 3.4 26.8 1.0
C A:GLU166 3.5 20.1 1.0
CD2 A:LEU167 3.6 25.3 1.0
CA A:LEU167 3.8 21.3 1.0
N A:LEU167 3.9 19.2 1.0
CG A:LEU167 4.1 23.6 1.0
C14 A:4WI401 4.2 19.7 1.0
CB A:MET165 4.2 18.2 1.0
CG A:MET165 4.3 18.8 1.0
N A:GLU166 4.4 16.1 1.0
O A:HOH564 4.4 26.6 1.0
SD A:MET165 4.4 27.8 1.0
O3 A:4WI401 4.5 19.7 1.0
C13 A:4WI401 4.5 19.8 1.0
CA A:GLU166 4.6 16.3 1.0
CB A:LEU167 4.6 21.4 1.0
NE2 A:GLN192 4.7 22.3 1.0
CB A:GLN192 4.7 22.3 1.0
CD A:PRO168 4.8 27.5 1.0
C A:LEU167 4.9 22.9 1.0
C A:MET165 5.0 16.5 1.0

Fluorine binding site 4 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:26.3
occ:1.00
F1 B:4WI401 0.0 26.3 1.0
C22 B:4WI401 1.3 27.1 1.0
F3 B:4WI401 2.1 30.2 1.0
F2 B:4WI401 2.2 28.7 1.0
C21 B:4WI401 2.4 21.0 1.0
O B:THR190 2.8 23.8 1.0
O4 B:4WI401 2.8 23.8 1.0
NE2 B:GLN192 3.0 17.8 1.0
CE B:MET165 3.2 27.1 1.0
N4 B:4WI401 3.5 19.7 1.0
CD B:GLN192 3.6 18.9 1.0
CG B:GLN192 3.7 18.4 1.0
O B:ARG188 3.8 18.6 1.0
CB B:GLN192 3.8 17.7 1.0
C B:THR190 3.9 22.5 1.0
N B:GLN192 4.1 20.4 1.0
N B:THR190 4.1 20.6 1.0
CD2 B:LEU167 4.4 22.2 1.0
SD B:MET165 4.6 31.3 1.0
CA B:GLN192 4.6 18.6 1.0
C B:ALA191 4.6 20.5 1.0
OE1 B:GLN192 4.6 17.1 1.0
CA B:THR190 4.7 21.4 1.0
O B:GLU166 4.7 18.0 1.0
C14 B:4WI401 4.7 18.4 1.0
CA B:ALA191 4.8 22.8 1.0
N B:ALA191 4.8 22.5 1.0
C B:ARG188 5.0 18.7 1.0

Fluorine binding site 5 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:28.7
occ:1.00
F2 B:4WI401 0.0 28.7 1.0
C22 B:4WI401 1.4 27.1 1.0
F3 B:4WI401 2.1 30.2 1.0
F1 B:4WI401 2.2 26.3 1.0
C21 B:4WI401 2.4 21.0 1.0
N4 B:4WI401 2.6 19.7 1.0
O B:GLU166 2.8 18.0 1.0
CE B:MET165 3.1 27.1 1.0
CD2 B:LEU167 3.4 22.2 1.0
C B:GLU166 3.4 15.9 1.0
O4 B:4WI401 3.5 23.8 1.0
CA B:LEU167 3.7 20.5 1.0
N B:LEU167 3.8 15.6 1.0
CB B:MET165 3.9 19.4 1.0
CG B:MET165 3.9 19.4 1.0
C14 B:4WI401 4.0 18.4 1.0
SD B:MET165 4.1 31.3 1.0
N B:GLU166 4.1 15.3 1.0
O3 B:4WI401 4.3 19.5 1.0
CA B:GLU166 4.4 16.1 1.0
C13 B:4WI401 4.4 18.0 1.0
O B:HOH571 4.4 24.3 1.0
CG B:LEU167 4.5 20.4 1.0
CB B:LEU167 4.6 19.5 1.0
C B:MET165 4.7 14.9 1.0
NE2 B:GLN192 4.7 17.8 1.0
CD B:PRO168 4.7 22.2 1.0
C B:LEU167 4.8 21.4 1.0
O B:THR190 4.8 23.8 1.0
C15 B:4WI401 4.8 22.0 1.0
CA B:MET165 4.9 15.6 1.0
CB B:GLN192 5.0 17.7 1.0

Fluorine binding site 6 out of 6 in 7vlp

Go back to Fluorine Binding Sites List in 7vlp
Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 Main Protease in Complex with PF07321332 in Spacegroup P1211


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 P1211 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:30.2
occ:1.00
F3 B:4WI401 0.0 30.2 1.0
C22 B:4WI401 1.2 27.1 1.0
F2 B:4WI401 2.1 28.7 1.0
F1 B:4WI401 2.1 26.3 1.0
C21 B:4WI401 2.3 21.0 1.0
N4 B:4WI401 3.0 19.7 1.0
O4 B:4WI401 3.1 23.8 1.0
O B:HOH571 3.4 24.3 1.0
O B:GLU166 3.4 18.0 1.0
CD B:PRO168 3.4 22.2 1.0
O B:THR190 3.7 23.8 1.0
CA B:LEU167 3.9 20.5 1.0
N B:GLN192 4.0 20.4 1.0
CD2 B:LEU167 4.2 22.2 1.0
N B:PRO168 4.2 21.2 1.0
C B:GLU166 4.3 15.9 1.0
C14 B:4WI401 4.3 18.4 1.0
C B:LEU167 4.4 21.4 1.0
CA B:ALA191 4.5 22.8 1.0
C B:THR190 4.5 22.5 1.0
N B:LEU167 4.6 15.6 1.0
CG B:PRO168 4.6 27.8 1.0
O B:GLN192 4.6 22.5 1.0
CB B:GLN192 4.6 17.7 1.0
C B:ALA191 4.7 20.5 1.0
CE B:MET165 4.7 27.1 1.0
C15 B:4WI401 4.8 22.0 1.0
CB B:LEU167 4.8 19.5 1.0
CA B:GLN192 4.8 18.6 1.0
N B:ALA191 4.9 22.5 1.0
C23 B:4WI401 5.0 21.9 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: Wed Jul 16 01:16:25 2025

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