Fluorine in PDB 8i30: Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J

Enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J

All present enzymatic activity of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J:
3.4.22.69;

Protein crystallography data

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J, PDB code: 8i30 was solved by R.Zeng, C.Huang, L.W.Xie, K.Wang, Y.Z.Liu, S.Y.Yang, J.Lei, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.78 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.249, 84.697, 51.479, 90, 115.14, 90
R / Rfree (%) 18.7 / 22.6

Other elements in 8i30:

The structure of Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J (pdb code 8i30). 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 the Sars-Cov-2 Main Protease in Complex with 32J, PDB code: 8i30:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 1 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


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 the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:50.3
occ:1.00
 F01 A:OF9401 0.0 50.3 1.0
C02 A:OF9401 1.4 51.3 1.0
F03 A:OF9401 2.2 60.8 1.0
C04 A:OF9401 2.3 55.1 1.0
C40 A:OF9401 2.4 53.3 1.0
C05 A:OF9401 2.9 46.7 1.0
C39 A:OF9401 3.0 42.2 1.0
C06 A:OF9401 3.5 52.4 1.0
CB A:MET165 3.6 33.2 1.0
O A:HIS164 3.7 38.2 1.0
CE1 A:HIS41 3.9 44.3 1.0
ND1 A:HIS41 4.0 37.4 1.0
SD A:MET165 4.0 42.6 1.0
CG A:MET165 4.2 34.3 1.0
C A:HIS164 4.3 28.1 1.0
NE2 A:HIS41 4.3 45.4 1.0
CA A:ASP187 4.4 42.2 1.0
C07 A:OF9401 4.5 50.9 1.0
O38 A:OF9401 4.6 48.8 1.0
CG A:HIS41 4.6 41.8 1.0
O26 A:OF9401 4.6 35.4 1.0
CB A:ASP187 4.6 36.0 1.0
CA A:MET165 4.6 32.1 1.0
C A:ASP187 4.7 50.2 1.0
CD2 A:HIS41 4.7 43.5 1.0
CB A:HIS164 4.8 29.9 1.0
N A:MET165 4.9 28.9 1.0
N A:ARG188 4.9 46.9 1.0

Fluorine binding site 2 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 2 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


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 the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:60.8
occ:1.00
 F03 A:OF9401 0.0 60.8 1.0
C02 A:OF9401 1.4 51.3 1.0
F01 A:OF9401 2.2 50.3 1.0
C40 A:OF9401 2.4 53.3 1.0
C04 A:OF9401 2.4 55.1 1.0
C A:ASP187 3.1 50.2 1.0
N A:ARG188 3.1 46.9 1.0
CE A:MET49 3.2 81.2 1.0
O A:ASP187 3.5 53.0 1.0
CA A:ARG188 3.5 57.8 1.0
CA A:ASP187 3.6 42.2 1.0
C05 A:OF9401 3.7 46.7 1.0
C39 A:OF9401 3.7 42.2 1.0
C A:ARG188 3.9 63.2 1.0
O A:ARG188 4.0 54.6 1.0
CB A:ASP187 4.1 36.0 1.0
C06 A:OF9401 4.2 52.4 1.0
SD A:MET49 4.6 90.8 0.7
N A:GLN189 4.7 73.3 1.0
O A:VAL186 4.7 34.9 1.0
ND1 A:HIS41 4.8 37.4 1.0
SD A:MET165 4.8 42.6 1.0
N A:ASP187 4.9 36.3 1.0
CG A:HIS41 4.9 41.8 1.0
CB A:ARG188 4.9 54.3 1.0

Fluorine binding site 3 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 3 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


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 the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:66.1
occ:1.00
 F11 A:OF9401 0.0 66.1 1.0
C10 A:OF9401 1.4 58.2 1.0
C09 A:OF9401 2.2 55.0 1.0
F12 A:OF9401 2.3 56.4 1.0
C13 A:OF9401 2.4 52.8 1.0
O A:HOH741 3.2 58.2 1.0
N08 A:OF9401 3.4 55.5 1.0
C14 A:OF9401 3.5 50.3 1.0
C15 A:OF9401 4.6 49.5 1.0
C07 A:OF9401 4.6 50.9 1.0

Fluorine binding site 4 out of 4 in 8i30

Go back to Fluorine Binding Sites List in 8i30
Fluorine binding site 4 out of 4 in the Crystal Structure of the Sars-Cov-2 Main Protease in Complex with 32J


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 the Sars-Cov-2 Main Protease in Complex with 32J within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.4
occ:1.00
 F12 A:OF9401 0.0 56.4 1.0
C10 A:OF9401 1.4 58.2 1.0
C09 A:OF9401 2.2 55.0 1.0
F11 A:OF9401 2.3 66.1 1.0
C13 A:OF9401 2.3 52.8 1.0
C23 A:OF9401 3.0 54.3 1.0
C14 A:OF9401 3.1 50.3 1.0
C24 A:OF9401 3.2 54.9 1.0
N08 A:OF9401 3.2 55.5 1.0
C15 A:OF9401 3.4 49.5 1.0
C22 A:OF9401 3.6 55.6 1.0
N16 A:OF9401 3.8 37.5 1.0
O37 A:OF9401 3.8 51.8 1.0
C19 A:OF9401 3.9 50.7 1.0
C21 A:OF9401 4.2 53.6 1.0
C20 A:OF9401 4.3 47.3 1.0
O A:HOH572 4.5 59.8 1.0
C07 A:OF9401 4.6 50.9 1.0
C17 A:OF9401 4.8 40.8 1.0
C18 A:OF9401 4.8 40.3 1.0
O A:HOH727 4.9 63.2 1.0

Reference:

C.Huang, R.Zeng, J.Qiao, B.Quan, R.Luo, Q.Huang, N.Guo, Y.Li, X.Long, R.Ma, A.Xia, Z.Fang, Y.Wang, Y.Li, Y.Zheng, L.Li, J.Lei, S.Yang. Discovery and Structure-Activity Relationship Studies of Novel Alpha-Ketoamide Derivatives Targeting the Sars-Cov-2 Main Protease. Eur.J.Med.Chem. V. 259 15657 2023.
ISSN: ISSN 0223-5234
PubMed: 37517202
DOI: 10.1016/J.EJMECH.2023.115657
Page generated: Fri Aug 2 20:32:35 2024

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