Fluorine in PDB 8hef: The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2

Enzymatic activity of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2

All present enzymatic activity of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2:
3.4.22.69;

Protein crystallography data

The structure of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2, PDB code: 8hef was solved by M.Yan, H.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.27 / 1.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.8, 99.06, 59.67, 90, 108.8, 90
R / Rfree (%) 13.3 / 17

Other elements in 8hef:

The structure of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 (pdb code 8hef). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2, PDB code: 8hef:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 1 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:17.8
occ:1.00
 F28 A:7YY401 0.0 17.8 1.0
C27 A:7YY401 1.4 15.3 1.0
C29 A:7YY401 2.3 16.2 1.0
C26 A:7YY401 2.4 15.1 1.0
C25 A:7YY401 2.8 15.2 1.0
CA A:GLN189 3.3 18.0 1.0
CB A:GLN189 3.4 20.8 1.0
O A:HOH744 3.5 31.9 1.0
O A:HOH708 3.5 35.6 1.0
CG A:GLN189 3.5 21.8 1.0
O A:HOH606 3.6 18.4 1.0
C30 A:7YY401 3.6 15.7 1.0
C34 A:7YY401 3.6 14.7 1.0
O A:HOH716 3.9 41.5 1.0
N A:GLN189 3.9 17.4 1.0
O A:HOH722 3.9 36.9 1.0
C32 A:7YY401 4.1 15.8 1.0
O A:ARG188 4.1 16.2 1.0
N24 A:7YY401 4.3 14.6 1.0
C A:ARG188 4.3 16.0 1.0
NE2 A:HIS41 4.5 16.9 1.0
CB A:MET165 4.6 17.5 1.0
CD A:GLN189 4.6 24.1 1.0
C A:GLN189 4.6 18.7 1.0
O36 A:7YY401 4.7 14.1 1.0
F31 A:7YY401 4.7 17.9 1.0
NE2 A:GLN189 4.8 23.4 1.0
SD A:MET165 4.8 18.9 1.0
C35 A:7YY401 4.9 14.7 1.0
CE1 A:HIS41 5.0 17.4 1.0

Fluorine binding site 2 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 2 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:17.9
occ:1.00
 F31 A:7YY401 0.0 17.9 1.0
C30 A:7YY401 1.4 15.7 1.0
C32 A:7YY401 2.4 15.8 1.0
C29 A:7YY401 2.4 16.2 1.0
F33 A:7YY401 2.7 14.0 1.0
CA A:ASP187 3.0 13.3 1.0
CB A:ASP187 3.0 12.1 1.0
C A:ASP187 3.1 15.1 1.0
ND1 A:HIS41 3.5 15.9 1.0
N A:ARG188 3.5 16.0 1.0
O A:ASP187 3.5 16.2 1.0
C34 A:7YY401 3.6 14.7 1.0
C27 A:7YY401 3.7 15.3 1.0
CG A:HIS41 3.7 15.2 1.0
CE1 A:HIS41 3.7 17.4 1.0
SD A:MET165 4.0 18.9 1.0
NE2 A:HIS41 4.1 16.9 1.0
CD2 A:HIS41 4.1 15.1 1.0
C26 A:7YY401 4.1 15.1 1.0
CB A:HIS41 4.2 15.1 1.0
N A:ASP187 4.4 12.8 1.0
OH A:TYR54 4.4 16.2 1.0
CA A:ARG188 4.4 17.1 1.0
O A:HOH617 4.4 13.7 1.0
CG A:ASP187 4.4 12.5 1.0
C A:ARG188 4.6 16.0 1.0
O A:ARG188 4.7 16.2 1.0
CD2 A:HIS164 4.7 11.9 1.0
O A:VAL186 4.7 13.1 1.0
CB A:HIS164 4.7 11.8 1.0
F28 A:7YY401 4.7 17.8 1.0
OD2 A:ASP187 4.9 11.9 1.0
CB A:MET165 5.0 17.5 1.0
C A:VAL186 5.0 12.1 1.0

Fluorine binding site 3 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 3 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:14.0
occ:1.00
 F33 A:7YY401 0.0 14.0 1.0
C32 A:7YY401 1.3 15.8 1.0
C30 A:7YY401 2.3 15.7 1.0
C34 A:7YY401 2.3 14.7 1.0
F31 A:7YY401 2.7 17.9 1.0
O A:HIS164 3.3 12.3 1.0
CB A:HIS41 3.4 15.1 1.0
CG A:HIS41 3.4 15.2 1.0
CD2 A:HIS41 3.5 15.1 1.0
SG A:CYS145 3.5 12.6 1.0
C29 A:7YY401 3.6 16.2 1.0
C26 A:7YY401 3.6 15.1 1.0
CB A:HIS164 3.8 11.8 1.0
C A:HIS164 3.8 12.3 1.0
CA A:HIS164 4.0 11.2 1.0
CD2 A:HIS164 4.0 11.9 1.0
C27 A:7YY401 4.1 15.3 1.0
ND1 A:HIS41 4.2 15.9 1.0
CG A:HIS164 4.2 12.7 1.0
O A:HOH617 4.2 13.7 1.0
NE2 A:HIS41 4.2 16.9 1.0
CL2 A:7YY401 4.4 15.5 1.0
CE1 A:HIS41 4.6 17.4 1.0
N A:MET165 4.8 12.7 1.0
CB A:MET165 4.8 17.5 1.0
CB A:ASP187 4.9 12.1 1.0
CB A:PRO39 4.9 12.0 1.0
C25 A:7YY401 4.9 15.2 1.0
CA A:HIS41 4.9 14.2 1.0
N24 A:7YY401 5.0 14.6 1.0

Fluorine binding site 4 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 4 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:18.6
occ:1.00
 F28 B:7YY401 0.0 18.6 1.0
C27 B:7YY401 1.4 16.6 1.0
C29 B:7YY401 2.4 17.6 1.0
C26 B:7YY401 2.4 15.6 1.0
C25 B:7YY401 2.8 14.7 1.0
O B:HOH827 3.1 27.3 1.0
CG B:GLN189 3.2 25.3 1.0
CA B:GLN189 3.2 21.4 1.0
CB B:GLN189 3.3 21.8 1.0
O B:HOH903 3.4 30.9 1.0
O B:HOH798 3.6 17.4 1.0
C30 B:7YY401 3.6 15.8 1.0
C34 B:7YY401 3.6 14.0 1.0
NE2 B:GLN189 3.7 29.5 1.0
CD B:GLN189 3.8 27.6 1.0
O B:HOH881 3.8 28.6 1.0
N B:GLN189 3.9 19.2 1.0
O B:ARG188 4.0 17.8 1.0
C32 B:7YY401 4.1 14.6 1.0
C B:ARG188 4.1 17.4 1.0
N24 B:7YY401 4.2 15.2 1.0
CB B:MET165 4.5 17.5 1.0
C B:GLN189 4.5 22.8 1.0
NE2 B:HIS41 4.6 14.3 1.0
O36 B:7YY401 4.7 15.1 1.0
OE1 B:GLN189 4.7 27.5 1.0
SD B:MET165 4.7 20.8 1.0
F31 B:7YY401 4.8 19.1 1.0
N B:THR190 4.9 22.1 1.0
C35 B:7YY401 4.9 14.8 1.0
CE1 B:HIS41 5.0 14.6 1.0

Fluorine binding site 5 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 5 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:19.1
occ:1.00
 F31 B:7YY401 0.0 19.1 1.0
C30 B:7YY401 1.3 15.8 1.0
C32 B:7YY401 2.3 14.6 1.0
C29 B:7YY401 2.4 17.6 1.0
F33 B:7YY401 2.7 15.1 1.0
CA B:ASP187 3.0 16.2 1.0
CB B:ASP187 3.0 15.3 1.0
C B:ASP187 3.2 16.9 1.0
ND1 B:HIS41 3.5 15.0 1.0
N B:ARG188 3.6 16.3 1.0
O B:ASP187 3.6 18.1 1.0
C34 B:7YY401 3.6 14.0 1.0
C27 B:7YY401 3.6 16.6 1.0
CG B:HIS41 3.7 13.2 1.0
CE1 B:HIS41 3.9 14.6 1.0
SD B:MET165 4.1 20.8 1.0
C26 B:7YY401 4.1 15.6 1.0
CB B:HIS41 4.1 13.2 1.0
CD2 B:HIS41 4.1 13.9 1.0
NE2 B:HIS41 4.3 14.3 1.0
O B:HOH866 4.3 13.8 1.0
CG B:ASP187 4.4 15.4 1.0
N B:ASP187 4.4 14.6 1.0
CA B:ARG188 4.5 19.1 1.0
CD2 B:HIS164 4.5 11.9 1.0
OH B:TYR54 4.5 15.2 1.0
CB B:HIS164 4.6 12.5 1.0
C B:ARG188 4.6 17.4 1.0
O B:ARG188 4.7 17.8 1.0
O B:VAL186 4.7 16.9 1.0
F28 B:7YY401 4.8 18.6 1.0
OD2 B:ASP187 4.9 13.7 1.0
CG B:HIS164 5.0 13.2 1.0
CB B:MET165 5.0 17.5 1.0

Fluorine binding site 6 out of 6 in 8hef

Go back to Fluorine Binding Sites List in 8hef
Fluorine binding site 6 out of 6 in the The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Crystal Structure of Deuterated S-217622 (Ensitrelvir) Bound to the Main Protease (3CLPRO/Mpro) of Sars-Cov-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:15.1
occ:1.00
 F33 B:7YY401 0.0 15.1 1.0
C32 B:7YY401 1.3 14.6 1.0
C30 B:7YY401 2.3 15.8 1.0
C34 B:7YY401 2.4 14.0 1.0
F31 B:7YY401 2.7 19.1 1.0
O B:HIS164 3.4 13.0 1.0
CB B:HIS41 3.4 13.2 1.0
CG B:HIS41 3.5 13.2 1.0
SG B:CYS145 3.5 12.2 1.0
CD2 B:HIS41 3.6 13.9 1.0
C29 B:7YY401 3.6 17.6 1.0
C26 B:7YY401 3.6 15.6 1.0
CB B:HIS164 3.8 12.5 1.0
C B:HIS164 3.9 12.5 1.0
CD2 B:HIS164 3.9 11.9 1.0
CA B:HIS164 4.0 11.8 1.0
C27 B:7YY401 4.1 16.6 1.0
O B:HOH866 4.1 13.8 1.0
CG B:HIS164 4.1 13.2 1.0
ND1 B:HIS41 4.2 15.0 1.0
CL2 B:7YY401 4.3 14.3 1.0
NE2 B:HIS41 4.4 14.3 1.0
CE1 B:HIS41 4.7 14.6 1.0
CB B:PRO39 4.8 11.0 1.0
CA B:HIS41 4.9 12.9 1.0
N B:MET165 4.9 13.7 1.0
C25 B:7YY401 4.9 14.7 1.0
CB B:CYS145 4.9 10.9 1.0
CB B:ASP187 5.0 15.3 1.0
CB B:MET165 5.0 17.5 1.0

Reference:

Y.Yang, L.Cao, M.Yan, J.Zhou, S.Yang, T.Xu, S.Huang, K.Li, Q.Zhou, G.Li, Y.Zhu, F.Cong, H.Zhang, D.Guo, Y.Li, X.Zhang. Synthesis of Deuterated S-217622 (Ensitrelvir) with Antiviral Activity Against Coronaviruses Including Sars-Cov-2. Antiviral Res. V. 213 05586 2023.
ISSN: ISSN 0166-3542
PubMed: 36997073
DOI: 10.1016/J.ANTIVIRAL.2023.105586
Page generated: Tue Apr 25 20:24:45 2023

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