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Fluorine in PDB 8hbk: The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir

Enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir

All present enzymatic activity of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir:
3.4.22.69;

Protein crystallography data

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir, PDB code: 8hbk was solved by M.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.26 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.093, 82.528, 51.526, 90, 115.13, 90
R / Rfree (%) 19.1 / 23.2

Other elements in 8hbk:

The structure of The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir (pdb code 8hbk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir, PDB code: 8hbk:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8hbk

Go back to Fluorine Binding Sites List in 8hbk
Fluorine binding site 1 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


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 Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.6
occ:1.00
F28 A:7YY401 0.0 39.6 1.0
C27 A:7YY401 1.3 38.5 1.0
C26 A:7YY401 2.3 36.2 1.0
C29 A:7YY401 2.4 40.5 1.0
C25 A:7YY401 2.7 34.2 1.0
CG A:GLN189 2.9 51.9 1.0
CB A:GLN189 3.1 40.4 1.0
CA A:GLN189 3.2 44.3 1.0
O A:HOH522 3.3 46.2 1.0
O A:HOH549 3.5 50.5 1.0
C34 A:7YY401 3.6 40.7 1.0
C30 A:7YY401 3.6 42.6 1.0
CD A:GLN189 3.7 54.6 1.0
O A:HOH543 3.8 40.5 1.0
N A:GLN189 3.8 36.9 1.0
NE2 A:GLN189 3.9 67.9 1.0
C32 A:7YY401 4.1 39.2 1.0
N24 A:7YY401 4.1 38.5 1.0
O A:ARG188 4.1 48.6 1.0
C A:ARG188 4.2 48.0 1.0
C A:GLN189 4.4 51.0 1.0
NE2 A:HIS41 4.5 30.6 1.0
CB A:MET165 4.6 39.4 1.0
O36 A:7YY401 4.6 34.1 1.0
OE1 A:GLN189 4.6 60.5 1.0
F31 A:7YY401 4.8 46.0 1.0
C35 A:7YY401 4.8 34.7 1.0
CE1 A:HIS41 4.9 41.0 1.0
SD A:MET165 4.9 40.0 1.0
N A:THR190 4.9 43.4 1.0
N12 A:7YY401 5.0 31.4 1.0

Fluorine binding site 2 out of 3 in 8hbk

Go back to Fluorine Binding Sites List in 8hbk
Fluorine binding site 2 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


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 Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:46.0
occ:1.00
F31 A:7YY401 0.0 46.0 1.0
C30 A:7YY401 1.4 42.6 1.0
C32 A:7YY401 2.4 39.2 1.0
C29 A:7YY401 2.4 40.5 1.0
F33 A:7YY401 2.6 33.5 1.0
CA A:ASP187 3.0 34.4 1.0
CB A:ASP187 3.0 31.4 1.0
C A:ASP187 3.2 42.2 1.0
O A:ASP187 3.5 37.8 1.0
ND1 A:HIS41 3.5 34.9 1.0
C27 A:7YY401 3.6 38.5 1.0
N A:ARG188 3.7 37.1 1.0
C34 A:7YY401 3.7 40.7 1.0
CG A:HIS41 3.8 38.5 1.0
CE1 A:HIS41 3.9 41.0 1.0
C26 A:7YY401 4.2 36.2 1.0
SD A:MET165 4.2 40.0 1.0
CB A:HIS41 4.2 36.0 1.0
O A:HOH565 4.3 32.4 1.0
CD2 A:HIS41 4.3 36.9 1.0
NE2 A:HIS41 4.3 30.6 1.0
CA A:ARG188 4.4 48.6 1.0
CG A:ASP187 4.4 33.3 1.0
N A:ASP187 4.4 28.6 1.0
OH A:TYR54 4.5 38.5 1.0
ND1 A:HIS164 4.5 32.8 1.0
C A:ARG188 4.5 48.0 1.0
O A:ARG188 4.6 48.6 1.0
CB A:HIS164 4.6 28.0 1.0
CB A:MET165 4.6 39.4 1.0
O A:VAL186 4.7 30.7 1.0
F28 A:7YY401 4.8 39.6 1.0
OD2 A:ASP187 4.9 32.0 1.0

Fluorine binding site 3 out of 3 in 8hbk

Go back to Fluorine Binding Sites List in 8hbk
Fluorine binding site 3 out of 3 in the The Crystal Structure of Sars-Cov-2 3CL Protease in Complex with Ensitrelvir


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 Sars-Cov-2 3CL Protease in Complex with Ensitrelvir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.5
occ:1.00
F33 A:7YY401 0.0 33.5 1.0
C32 A:7YY401 1.3 39.2 1.0
C30 A:7YY401 2.3 42.6 1.0
C34 A:7YY401 2.4 40.7 1.0
F31 A:7YY401 2.6 46.0 1.0
O A:HIS164 3.3 38.2 1.0
CB A:HIS41 3.3 36.0 1.0
CG A:HIS41 3.4 38.5 1.0
C29 A:7YY401 3.6 40.5 1.0
CD2 A:HIS41 3.6 36.9 1.0
SG A:CYS145 3.6 33.8 1.0
C26 A:7YY401 3.6 36.2 1.0
CB A:HIS164 3.8 28.0 1.0
C A:HIS164 3.9 31.9 1.0
ND1 A:HIS164 3.9 32.8 1.0
CA A:HIS164 4.0 30.4 1.0
C27 A:7YY401 4.0 38.5 1.0
O A:HOH565 4.0 32.4 1.0
ND1 A:HIS41 4.1 34.9 1.0
CG A:HIS164 4.3 29.7 1.0
NE2 A:HIS41 4.3 30.6 1.0
CL2 A:7YY401 4.5 36.8 1.0
CE1 A:HIS41 4.6 41.0 1.0
CB A:MET165 4.6 39.4 1.0
CB A:PRO39 4.8 25.6 1.0
CA A:HIS41 4.8 34.9 1.0
CB A:ASP187 4.8 31.4 1.0
N A:MET165 4.9 31.5 1.0
C25 A:7YY401 5.0 34.2 1.0

Reference:

Y.Duan, H.Zhou, X.Liu, S.Iketani, M.Lin, X.Zhang, Q.Bian, H.Wang, H.Sun, S.J.Hong, B.Culbertson, H.Mohri, M.I.Luck, Y.Zhu, X.Liu, Y.Lu, X.Yang, K.Yang, Y.Sabo, A.Chavez, S.P.Goff, Z.Rao, D.D.Ho, H.Yang. Molecular Mechanisms of Sars-Cov-2 Resistance to Nirmatrelvir. Nature 2023.
ISSN: ESSN 1476-4687
PubMed: 37696289
DOI: 10.1038/S41586-023-06609-0
Page generated: Fri Aug 2 20:06:54 2024

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