Fluorine in PDB 7xar: Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor

Enzymatic activity of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor

All present enzymatic activity of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor, PDB code: 7xar was solved by J.M.M.Caaveiro, J.Ochi, D.Takahashi, T.Ueda, A.Ojida, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.07 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.027, 63.362, 102.831, 90, 90.4, 90
R / Rfree (%) 17.3 / 20.6

Other elements in 7xar:

The structure of Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Nickel (Ni) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor (pdb code 7xar). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor, PDB code: 7xar:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7xar

Go back to Fluorine Binding Sites List in 7xar
Fluorine binding site 1 out of 4 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:23.4
occ:1.00
 F13 A:BOV406 0.0 23.4 1.0
C12 A:BOV406 1.4 20.9 1.0
C11 A:BOV406 2.4 19.9 1.0
C14 A:BOV406 2.4 19.7 1.0
C10 A:BOV406 3.1 18.7 1.0
CG A:GLN189 3.3 32.7 1.0
N A:THR190 3.4 26.8 1.0
C A:GLN189 3.4 29.4 1.0
C17 A:BOV406 3.7 18.0 1.0
C15 A:BOV406 3.7 19.0 1.0
CA A:THR190 3.8 26.4 1.0
O A:GLN189 3.8 26.7 1.0
CA A:GLN189 3.9 28.5 1.0
C A:THR190 3.9 25.9 1.0
C16 A:BOV406 4.2 19.3 1.0
CB A:GLN189 4.2 31.4 1.0
N A:ALA191 4.2 25.4 1.0
O A:THR190 4.3 25.7 1.0
C09 A:BOV406 4.3 17.7 1.0
CD A:GLN189 4.5 34.6 1.0
N18 A:BOV406 4.6 18.0 1.0
O A:HOH659 4.7 22.4 1.0
NE2 A:GLN189 4.9 37.7 1.0

Fluorine binding site 2 out of 4 in 7xar

Go back to Fluorine Binding Sites List in 7xar
Fluorine binding site 2 out of 4 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F406

b:24.6
occ:1.00
 F33 A:BOV406 0.0 24.6 1.0
C32 A:BOV406 1.4 23.2 1.0
C30 A:BOV406 2.3 21.6 1.0
SG A:CYS145 2.6 22.8 1.0
O31 A:BOV406 2.7 20.1 1.0
CB A:CYS145 2.9 17.8 1.0
O A:HOH626 3.3 31.4 1.0
O A:HOH574 3.3 39.7 1.0
CD2 A:HIS41 3.4 21.9 1.0
NE2 A:HIS41 3.6 22.4 1.0
N22 A:BOV406 3.6 19.2 1.0
O A:HOH694 3.7 30.3 1.0
N21 A:BOV406 4.1 18.1 1.0
CA A:CYS145 4.1 16.1 1.0
N A:CYS145 4.1 15.0 1.0
CD2 A:LEU27 4.2 17.2 1.0
CB A:LEU27 4.2 16.1 1.0
N A:GLY143 4.4 17.3 1.0
CA A:GLY143 4.4 17.1 1.0
C19 A:BOV406 4.6 19.0 1.0
CG A:HIS41 4.7 20.3 1.0
O20 A:BOV406 4.7 19.6 1.0
C A:GLY143 4.7 15.9 1.0
O A:THR26 4.8 22.6 1.0
CG A:LEU27 4.8 17.1 1.0
C23 A:BOV406 4.8 21.6 1.0
CE1 A:HIS41 4.8 21.7 1.0
N A:SER144 5.0 15.8 1.0

Fluorine binding site 3 out of 4 in 7xar

Go back to Fluorine Binding Sites List in 7xar
Fluorine binding site 3 out of 4 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:27.6
occ:1.00
 F13 B:BOV403 0.0 27.6 1.0
C12 B:BOV403 1.4 27.0 1.0
C11 B:BOV403 2.4 25.3 1.0
C14 B:BOV403 2.4 26.6 1.0
C10 B:BOV403 3.0 25.4 1.0
O B:GLN189 3.2 26.7 1.0
C B:GLN189 3.2 29.2 1.0
N B:THR190 3.5 29.3 1.0
C17 B:BOV403 3.7 24.6 1.0
C15 B:BOV403 3.7 26.9 1.0
CA B:THR190 3.8 30.9 1.0
CA B:GLN189 3.9 29.9 1.0
C B:THR190 3.9 30.9 1.0
CB B:GLN189 4.1 33.0 1.0
C16 B:BOV403 4.2 26.0 1.0
O B:THR190 4.3 28.1 1.0
N B:ALA191 4.3 31.7 1.0
C09 B:BOV403 4.4 24.1 1.0
O B:HOH728 4.5 28.5 0.6
N18 B:BOV403 4.6 23.2 1.0
OE1 B:GLN189 4.7 29.5 1.0

Fluorine binding site 4 out of 4 in 7xar

Go back to Fluorine Binding Sites List in 7xar
Fluorine binding site 4 out of 4 in the Crystal Structure of 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor


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 3C-Like Protease From Sars-Cov-2 in Complex with Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:32.2
occ:1.00
 F33 B:BOV403 0.0 32.2 1.0
C32 B:BOV403 1.4 29.7 1.0
C30 B:BOV403 2.3 27.0 1.0
O31 B:BOV403 2.6 27.7 1.0
SG B:CYS145 2.8 26.3 1.0
CB B:CYS145 3.1 20.8 1.0
O B:HOH664 3.6 29.8 0.6
CE1 B:HIS41 3.6 39.4 1.0
N22 B:BOV403 3.6 24.5 1.0
ND1 B:HIS41 4.0 34.8 1.0
N21 B:BOV403 4.1 24.6 1.0
N B:CYS145 4.1 16.8 1.0
N B:GLY143 4.2 18.2 1.0
CB B:LEU27 4.2 17.4 1.0
CA B:CYS145 4.2 17.1 1.0
CA B:GLY143 4.2 17.5 1.0
CD2 B:LEU27 4.2 18.1 1.0
C19 B:BOV403 4.6 24.9 1.0
C B:GLY143 4.7 17.3 1.0
O B:THR26 4.7 21.9 1.0
O20 B:BOV403 4.8 25.5 1.0
NE2 B:HIS41 4.8 40.9 1.0
CG B:LEU27 4.8 16.8 1.0
C23 B:BOV403 4.8 25.3 1.0
N B:SER144 4.9 16.8 1.0

Reference:

Y.Hirose, N.Shindo, M.Mori, S.Onitsuka, H.Isogai, R.Hamada, T.Hiramoto, J.Ochi, D.Takahashi, T.Ueda, J.M.M.Caaveiro, Y.Yoshida, S.Ohdo, N.Matsunaga, S.Toba, M.Sasaki, Y.Orba, H.Sawa, A.Sato, E.Kawanishi, A.Ojida. Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors For Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease. J.Med.Chem. V. 65 13852 2022.
ISSN: ISSN 0022-2623
PubMed: 36229406
DOI: 10.1021/ACS.JMEDCHEM.2C01081
Page generated: Fri Aug 2 15:22:04 2024

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